I just tried to run two escalating nightmare dungeons in a row where the first dungeon requirement was to kill animus carriers and ollect animus to unlock the next door to continue. In both cases after clearing every enemy available i have ended up one animus short from whats required to open the door. There is no blue mark on the map showing a missed anima on the ground, ive ran back though every corridor two or three times to see if i could find anything and even left and re-entered to see it it could reset something.
From what i have seen this has been reported before and the causes were thought to be either an interaction with the barbarian charge skill (i am running a charge build) or killing an animus carrier too close to the boundary wall.