I've been reporting this bug since the early days of FE. Stardock has no plans to change it. Whenever you load from a saved game, all of your units will move if they had been previously been given a move assignment before you saved. That will results in all kinds of chaos such as you and enemy units standing on the same tile. I think you've also pointed out a related issue that if you get attacked while you have a previous move assignment, then you will end up standing on the lair tile without looting it. Since I've been telling them to fix it since early FE, I wouldn't get my hopes up.
Ahhh. Yeah, that makes more sense as an explanation.
I believe the problem is specifically loading from the Autosave.