Game Issues
Menu Items Reload Constantly Creating A Flashing Effect
Unclear what triggers this, but menu items can get stuck in a loop after opening, where they constantly open and close creating a strobe/flashing effect.
Launching Pokémon Go from a raid invite notification causes overlay issues

When launching Pokemon Go from a raid invite and going straight into that raid the games main overlay (Pokeball Menu, nearby, quests etc) all remain on top of the raid interface and fully interactable.
Elite Raids

Elite Raids have had several issues with their launch including the fact they were blocking/blocked the Community Day eggs at the time. For the second round of Elite Raids, Niantic instead spawned them after Community Day eggs instead of the 24-hour timer they were supposed to have. If you were doing one of the Community Day raids when the Elite Raids would spawn, you would be unable to complete the raid, and kicked out as if you lost the raid (your pass would be taken). If you try to do the Elite Raid the next day, it claims you have already used a pass. During the second round, many trainers reported they couldn't actually finish the raid, with the HP going to 0 but the raid never finishing. Other issues reported were once you completed the raid, after throwing the first ball, Hoopa would instantly run. You could then go back into the raid, and try to catch Hoopa again, but it would always run on the first ball. One of the main issues was the 'bonus' that Niantic told people to stay around the gym for, but then silently removed any mention of it from their articles. After the raid was complete, the BCR of one of the Kanto birds (depending on the time the Elite Raid took place) was increased significantly making it harder to catch. This happened during the second round of Elite Raids as well. At this point some trainers had a 15-minute timer appear, and some had the timer appear twice. Some received rare spawns such as Galarian Mr. Mime. Some saw the Kanto birds. Some attempted to catch one of these Pokemon and it would disappear. If you did get the rare spawns and walked more than about 20 meters away from the gym, the spawns would disappear. If you were tracking one of these rare spawns, the nearby list would glitch out and show you tracking two separate Pokemon. Niantic has completely ignored the issues, and hasn't acknowledged anything regarding these spawns so it is not clear what was supposed to happen. Niantic had a second round of Elite Raids on November 13th, which appears to have fixed nothing from the first round of issues. Niantic has still not acknowledged any of these issues.
Map Glitches And Changes Ground Texture
After the Halloween map update, the map will glitch out and change ground textures for about a second seemingly randomly. This has not been acknowledged by Niantic.
Absol with Sunglasses Mega Evolution icon missing

Absol with Sunglasses, when Mega Evolving, gltiches the Mega Evolution icon, sometimes missing, or appearing as other Pokemon. Other costumed Pokemon, such as Blastoise and the Gengar costumes behave normally. Image via u/zapellat on /r/thesilphroad.
Hatched Filter Shows Pokémon From Other Sources

Unclear as to why this happens, but Pokemon are sometimes counted as hatched, even though they can not be hatched (like Legendary Pokemon).
Pokémon Evolution Is Missing Its Background

The blue background for evolving a Pokemon has been missing since 249.
Cosmog Was Transferrable
The transfer issue has now been fixed, but for two weeks it was possible to transfer your only Cosmog. Evolving Cosmog was required to complete the special research at the beginning of October. When Niantic Support was contacted, they refused to give trainers a replacement Cosmog as we will be getting another at some point in the future. These trainers are still unable to complete their research. Niantic has since changed the quests to not require a Cosmog for evolution. But trainers still do not have their replacement Cosmog.
GO Plus Catches Not Counting Daily Adventure Incense For Research
Niantic's known issues described the bug as 'Issue description: Pokémon attracted to Daily Adventure Incense caught using a PGP or PBP will not appear on the summary screen or count towards Special Research.' and that it was fixed in 247. It was fixed for the summary screen, but not for special research. This has not been acknowledged.
Mega Evolved Pokemons icon does not change
When Mega Evolving a Pokémon the sprite in your storage will not update until you leave and reload your storage. If you have a mega evolved Pokémon and mega another Pokémon neither the old or new sprites change until a reload. This has been an issue for some time. The date is placeholder.
Community Day Raid Bonus Spawns
This has been an issue since they launched, but there have been continued reports of spawns disappearing when another egg appears in the same cell, or spawns disappearing when tapped, or not spawning at all. For the most part, it does work as advertised, but there are some rough edges that still need to be ironed out. Niantic did report this issue was fixed, but there are still reports of issues.
Defeating an Ultra Beast Doesn't Count Towards Some Research
Ultra Beats in raids do not count towards quests such as "Win a 3-star or higher raid”.
When A Mega Evolution's Timer Runs Out, You Are Kicked From The Raid
During a raid, when you have a Mega-evolved Pokemon in the lobby and have it in your team, and the timer expires on it, once the raid starts, it will kick you out on the GO screen, and back to the overworld map.
Healing Pokémon With Golden Razzberries Often Does Not Work
When healing Pokemon with a Golden Razzberry at a gym, it can often take 3-4 Golden berries before the healing effect is applied. It is unclear what triggers this, or what causes it to eventually work.
The Game Crashes On Android When Attaching A File To A Support Chat
The game will crash if you try to attach a file to a support chat on Android. Unclear when this started, so the time is an estimate.
Recently Fixed
Starly's Wings Are Broken

Like Pidgey before, it has no wings. Probably been broken since the Unity 2021 update. This was fixed at some point but we weren't sure when.
Premier Balls are Usable in the Wild and Quests

By doing a raid or rocket, then tapping on a wild Pokemon with remember the last ball enabled, the premier ball comes up. If you try to catch the Pokemon with it, it runs (but just visually).
269 Crashes On Start
Some Android devices are crashing on 269 when they boot up. Fresh installs or going back to 267 appear to be the workarounds. Niantic acknowledged they are looking into it.
Blanche Research Reset
At the end of the Blanche event, everyone's special research reset if they didn't complete it. Niantic acknowledged this issue and promptly auto-completed people's research to get based this step for them.
Blanche Lapras not added
Niantic has not pushed the assets for Blanche Lapras causing the encounter to error when loading that encounter, making it uncatchable.
April Quests Never Re-Rolled
Niantic forgot to re-roll new quests for April. They eventually realized this and fixed it on April 3th.
Willow Ticket can't be gifted

The Willow ticket can not be gifted and shows as the GO fest ticket in players' inventory. This was fixed to be giftable on the 1st, but it was using the wrong sprite. They fixed the sprite the next day.
Gimmighoul

Gimmighoul's stats were copy and pasted from other Mons without being checked, so it is very broken. Wrong buddy/walked stats, wrong evo requirements, wrong third move, probably wrong BCR and BFR, wrong sizing, and more. This has been partially fixed but some issues still remain.
Game Freezes Trying to Claim Scatterbug
Since 261, there is a high chance the game will freeze when claiming a Scatterbug from the pop-up notification. Niantic has not acknowledged this issue but there were no reports of this since .3.
Friends List Issues

Since 261, the friend list's avatars appear to be double rendered, and moving left to right in your friends list info screen glitches for a second and shows you the previous friend's avatar and buddy. Niantic has not acknowledged this issue but it doesn't appear to happen since .3.
Raids Are Unresponsive And Second Charge Moves Don't Work

In 261, raids can become unresponsive with taps not showing and your Mon standing still. It appears to still be doing damage, but your second charge move won't charge and your first charge move won't fire. If your Mon faints, you can be stuck in an unresponsive state for 30+ seconds. This appears to happen randomly, from reports about 1/5 raids. From further reports, it appears to be triggered when you use a Mon with a second charge move, where the second move won't charge/fire, and then the other issues start. Niantic never acknowledged this issue, but there haven't been reports of it in a while so marking as fixed.
Can't Search Mega Levels
When Niantic pushed the new Mega settings for Primals, they broke the ability to use search filters like `mega1`, `mega2`, etc. Niantic removed the text for the new Pokedex which fixed this issue.
Battle Parties Do Not Sync
Niantic launched the Battle Party feature on December 7th, 2017. At that time, they announced Battle Party syncing between devices. It never came. Several years later, they announced that Battle Party sync was now available, but it was never activated. The feature is still not active today.
Quest Stamps Are Double Rendered

Like the friends list, the quest stamps are double rendered, making it difficult to tell if you have completed your stamp for the day or not. This was fixed in 261.1.
Kecleon Issues
For the most part Kecleon was a successful rollout without any game breaking bugs. There were a few issues, some of which Niantic has acknowledged. They include: It uses Meltan's cry (not acknowledged), it has no gender so it was disabled being sent to HOME, sometimes it doesn't appear on the map after being attacked, and Niantic says this is an issue - you can see Kecleon when outside the stop's radius. The cry and gender has been fixed and on Jan 31 they re-enabled HOME sending.