I played a bunch of missions now, and I must say I really HATE this new aleph collecting! It's BAD because it totally breaks the flow of the game, everytime you have to look around for the Aleph drop! And others can steal it from you (elite/ raiders). And no one can deny that this mechanic in the current state is worse than before (no one can say I'm stubborn, but this mechanic is just bad implemented right now).
"If it ain't broke, don't fix it"
Auto-take what you need on ammo an leave the rest on the field, but totally revert back the old aleph collecting (for healing purpose too!).