I'm having the same problem. Even when I kill one of the mechs before it calls for reinforcements, I still don't have enough ammo to kill the remaining mechs. Did you ever find a solution to this?

I have over 200,000 upgrade points but I cannot upgrade the staff because the girl isn't around.

Edit: Nevermind. When I killed the 2nd last enemy, more ammo spawned.

I got it after upgrading my staff to extra damage (you can use chapter select for this I think - but you might have to replay the rest of the level).