I noticed that if, for some reason, the /kill command is set to kill the player from a repeated command block, it may cause the player to be unable to pause due to being killed too fast to register inputs if the command came from an active repeating command block.

The more command blocks that cause this to occur, the more likely it'll be that you won't be able to pause(or the pause screen gets exited due to respawning). Lower framerates seem to help circumvent this to some extent, though.

Clarification: this only happens of doImmediateRespawn is set to true.