On two attempts, after completing "Defeat the second wave of attackers" on the Aiden Path, he proceeded to appear to lose
all AI - even after clearing all enemies on my compass, or when another wave spawned, he just stood there where he was.
Interestingly, at this point, so did Lupe. Even when she took a Molotov to the head from one of the (apparently infinitely spawning) waves of guys coming out the front doors.
Observe:
Aiden
did shout "follow me" or something to that effect at me when that quest-stage activated, but that was it.
Testing Jake Path now to check it didn't break too.
EDIT: Alright, yeah, on the Jake Path too, both Lupe and Aiden both go braindead as soon as that quest stage is reached, not even reacting to trying to Talk to them (that's why I went right up to Aiden in the video above). Jake still acts as a valid 'Stimpak Target' companion (on both paths), but nobody else does.