I've had that problem too.  Usually occurred when I tried to attack a stack of dudes that were already dead because I used pillar of flame on them.  That caused my End Turn button to disappear and then I had to reload from save.  What made it even more annoying is that when I first loaded from that save, Altar would surrender to me even though he was winning 475 to 100.  That pillar of flame bug is a nasty one!  So I had to go back two saves.  Argh!

Trojasmic I think that was what happened with me too. I pillar of flame some groups and it appears to kill them but they don't disappear, and regenerate some HP the next turn.

It's not always an auto move problem as I have had this countless times with units from my side and the AI's that are still trying to move - the dreaded "running man".  If you check out the map and find one of your units running on the spot click on them an reissue or cancel the move order and the turn button re reappears.  If it's one of the AI units then usually a reload will free it up, but sometimes a particular obstruction in the world will cause this to happen again & again.

Hopefully this will be fixed soon, as it has been a problem for some time.

I have had the issue a few more times *possibly associated with the running man* but I have always managed to work my way out of the bug.

This is happening to me in the latest build every 20 mins or so, the whole UI is disabled not just end turn button. I can still move units and build in cities but not recruit and have to alt F4 and reload an auto save, very frustrating!