The physics engine is pretty awful. The connectors can't decide whether they're free or fixed, and sometimes the craft turns inside-out for no reason.
Also, there's no easy way to remove a part from the build area. The closest that I could find was to select it, then select the engine.
I just found a glitch on level 8. The Golgi Body ceases to take build orders, so I can't increase Defensin or make Toxins.
...and just now, it started working again. That was weird.
The game itself seems fun, but it's terribly unresponsive. Especially if it's going to have a timer, it needs to only take 1 button push per move, instead of 2-6.
Re: 39: You have to bank the first fireball into the side hole, and get it to light the bottom torch (it has to bounce off a bottom thing instead of falling thru). If it doesn't, then suicide and restart. Use the second fireball to light the top torch, which is easy.