Tokens controlled by a player and with sight will always stay in front of tokens without those properties - this is intentional, and not a bug. It stops players from being able to lose their tokens. Leaving "has sight" ticked on NPCs is generally not a good idea unless for some reason you need it - they add to the Dynamic Lighting calculations and can slow the map down considerably for the players if all the NPCs have it on. Even if a token has "has sight" ticked, it will still usually need to be either controlled by a player, or linked to a character sheet to which a player has control, to be automatically brought to the front. If the NPC has no player permissions set, you should be able to send the token to the back.
