I had to implement some unsatisfying hacks to make my Scratch shooter work as well! If I remember correctly I was manually duplicating the master projectile and I had to register each projectile against each enemy.
Megaman could apparently only shoot N bullets at once (3 or 5, I forget). Thus, they only ever had 5 bullet objects, iterated through a list to see if the bullet was shot or not, and only let you fire if there was a spare bullet.
I thought it was very clever. Sounds like you did much of the same thing.
https://www.evernote.com/shard/s4/sh/90b814fd-df52-4fcf-9127...