BUG (1.22) I've noticed that there seems to be a bug in relatively early waves (pre 350). When you have enough firepower to kill everything as it enters the screen your progression slows dramatically. I know about the bug fix to prevent 1 ship for counting as an entire formation so it could be something to do with that.
I've frequently found myself waiting with 1 formation left for 10-15 seconds while I'm seeing just a wall of explosions (usually due to Rad Clouds and Blackhole) and my fighters/bombers/regular weapons fire rarely but it won't let me advance until an enemy get a chance to fully appear before it dies.
there is currently a bug with the experimental capacitors that disables pause and lets heat of vents go past their limit as well as letting fuel cells go into negative.