I had several (I think it was three) suspicious keys on the ground. When I built a small key shack, I somehow ended up with two keys in storage but seemingly inaccessible, and one key in storage normally. The two keys I cannot access claim to be in storage based on the top screen inventory menu, but are not visible in the storage menu for the small key shack, nor do they appear in the visual change for the key shack.
I do not know how the keys were lost since I was not watching my villagers try to store them, and only realized there was an issue afterwards.
I encountered a similar issue several months ago, but thought the two keys had been placed in some other building and I just wasn't finding them (I checked this time and I don't think any buildings other than the key shack and loot boxes have a storage slot for suspicious keys). Since this has now happened twice I think it's probably a bug.
Update: I followed an organizer from picking a key up off the ground, putting it in the key shack, picking it up from the key shack, storing it in a lootbox, then walking back to the key shack to pick up a second key to try and put in the same lootbox (the lootbox the organizer opened was the only one on the map at the time). This is where the problem shows up - the organizer picked up the key from the shack, but the lootbox had disappeared, so they switched to another task without putting the key down. They picked up dirty water buckets while still carrying the key, and dropped everything off at the water purifier. This created a storage slot for keys in the water purifier. I checked through my other buildings and found another key in my crystal harvestery, so presumably the others are hiding somewhere else in my village.
So, the actual bug is that organizers try to put suspicious keys in a loot box that has already been opened, and then drop the key at the next location they're depositing resources, which creates storage slots for suspicious keys in buildings that should not be able to store them.