Squids and Guardians (possibly as well as other mobs) are despawning despite being named via a name tag or spawn egg. Named Squids and Guardians are spawned into (separate) pools of water. Upon exiting the chunk and returning, all have despawned.

To reproduce bug:

1. Spawn a guardian or squid into a pool of water
2. Name the mob, either by using a name tag or spawning it with a spawn egg
3. Leave the chunk and return
4. Mob will no longer be present