hello,
well on none of the 2missions it was an "aleph use" problem.
on beast's lair (not sure of the name in english) we were stuck on the mission, the boss was dead, (well, he had no more health at all), but the game let the mission continue as if he was still alive. we could still shoot him, or put aleph in "Pig", what we did several times, but it changed nothing.
we were just stuck like that until we ran out of live.
and on "upside down" mission, "mission failed" appeared all of a sudden, pretty early in the mission, whereas there was no reason for it.