so its a good game. ive noticed the missle blip (maybe you could make it so the missles and stuff stop at the end of level? or player invincible for the breaks?
i didnt notice the money bug (lol that made a funny image in my imagination) but it might be true as i didnt seem to have as much money is i thought i had worked out in my head after i had spent some on something.
through out the game i saw tht the enemys dropped like a randow amount or materials (1lvl i got over 100 mats, next lvl i got about 50) maybe you could define an upper and lower limit o the materials dropped per enemy type? (eg crap thing drops 5-15, medium craft drops 20 - 30, missile one drops 35-50 and bosses should drop 75-100 or what ever) that would make the game a tad easier especially as the upgrades near the end (which really are needed) cost a reasonable amount, but you fight have to fight through 3-5 rounds to get enough for them.
if you have a look at these problems nd maybey more which other people have identified and fixed them then i will play till this game is dead :)