I've experienced this a few times but most recently I had a Dreadhorde butcher and mayhem devil in hand with a cauldron familiar, a phyrexian tower, blood crypt, the green half of a pathway and a stomping ground in play. When I played the devil with auto-tap I figured it would use the crypt, the stomping ground and either of the other two lands. Instead it used the crypt and sacrificed the familiar, leaving me unable to cast the butcher with just the stomping ground and pathway left in play.

I was able to recover that game but I've lost before when, despite having access to enough mana, Phyrexian tower decides to sacrifice a creature for 2 mana rather than tapping a second land.

Off the top of my head the problem would be solved if you removed the sacrifice ability from being able to be selected with auto-tap, or force the player to choose which creature when auto-tapping rather than it being chosen at random or of course stopping it from auto-tapping all together would work as well.