Game Issues
Wrong "Team Mystic" Logo used for Ditto Sticker

When the game was originally released, a fan recreated the Team Mystic logo, and misinterpreted it's shape. The Ditto sticker is based on the fan-made Team Mystic logo, instead of the official one. While this could be seen as a "mistake made by Ditto", it's most likely a mistake made by the designer of the sticker.
Research Icon Stays Orange After Completing Referral Quests
If you use someone's referral code to join/come back to the game, and complete all the Quests for it, your Quest icon is stuck orange, in the quest completed state and is impossible to recover from. When Niantic support has been contacted, they have dismissed the issue.
Powered Up Pokestop Bonus Spawn
After launching the Powered Up Pokestop feature in beta for a short while, they released it worldwide. One of Level 3's rewards was a bonus Pokemon spawn around the stop or gym once fully powered up, but after this feature was rolled out worldwide, trainers discovered this feature was broken. When you would load the map with one of these spawns active, it would prevent your map from loading, as well as preventing you from catching Pokemon. Niantic responded by temporarily disabling that bonus, with intentions to fix it. They disabled it around December 10th, 2021 and it has not been re-enabled since.
Trainer Name Is Not Visible In Gyms Next To Large Pokémon

In the 215 release notes, Niantic said 'Fixed bug causing Trainer avatar to appear to the side of the Gym screen when a large-sized Pokémon is placed as a Gym defender.' In 217 this broke again and has not been acknowledged since.
Costumed Raid Boss Pokémon lose costume if caught after the end of a special event.
A costumed Raid Boss during a special event will lose its costume if it is caught after the event ends, even if the Raid Battle takes place right before the end time of the event. This issue actually appeared on the Niantic "Known Issues" tracker, and was removed in October 2021, but was never fixed (or was broken again after it was fixed). Pokemon still lose their costumes if caught after the special event ends.
Mega Pokémon Do Not Have Feeding Animations
Mega Pokemon do not have feeding animations when feeding in Buddy Adventure. This was acknowledged by Niantic as an issue but nothing has been done since to fix it.
Scrolling Your Pokemon Storage Is No Longer Smooth
The earliest report of this issue we can find is on August 6th, 2020. Scrolling Pokemon in the storage menu used to be the traditional 'smooth' scrolling most mobile devices are used to. Specifically, when you scroll up or down and release your finger, the scroll keeps going for a little bit before slowing down. However around the reported date, it broke and the scroll abruptly stops when you lift your finger instead, making scrolling more difficult. This appears to be an issue for accounts with a large number of Pokemon in their storage.
Incense Spawns Overlapping With The Trainer
Niantic made an update shortly after COVID began to move incense Pokemon away from the trainer when they spawned. This worked for a few updates, but then broke and hasn't been acknowledged since. The date is an approximation as we aren't sure exactly when it broke.
Poffin Buff on a Pokemon resets at midnight
If you have buddy Pokemon you have fed a Poffin to it will lose the Poffin buff regardless of time remaining at midnight.
Nesting Pokémon Blocks Low Dex Number Spanws
If a Pokemon can nest but isn't currently the nest pokemon of a given nest, and its dex number is low, that Pokemon will not spawn at all in the nested area. This has been reported with Pokemon such as Pikachu, the Kanto starters and more. This has been going on for a long time, so the estimate is based on the earliest date we could find this reported.
Profile Page Scrolls Back To The Top When The Plus Catches A Pokémon
If you are looking at a medal or scrolled down on the Trainer Profile page, and your plus catches a Pokemon, the page scrolls back up to the top.
Kids Account Auto Complete Quests Are Inconsistent
Certain field tasks relating to friends, such as adding new friends or sending gifts to friends auto-complete themselves on Kids account. However, some event-limited friends field task doesn't auto-complete, making them impossible to complete unless the parents have enabled friend activity in the PTC portal.
Battery Saver Causes Assets To Not Load

By using Battery Saver mode, then tilting up in-game on a pokemon screen, then swiping, random assets will unload. Typically the CP, HP, certain letters of names, weight, size, and others will disappear. Sometimes only / characters will be removed. Closing storage fixes it. Unclear when this started, but our guess is since the beginning of time.
Flying Pokémon Reset Their Height After Breaking Out
This has been an issue since additional animation types were added to the game. If you throw a ball at a flying Pokemon in the upper position, and it breaks out, its hitbox is still positioned at the upper position, even though its model is in the lower position.
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.