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:
Spawn a guardian or squid into a pool of water
Name the mob, either by using a name tag or spawning it with a spawn egg
Leave the chunk and return
Mob will no longer be present
Couldn't confirm for MC 1.13-pre3.
Cannot reproduce.