Found a glitch. Sometimes when I start a new game I somtimes shoot big bullets (like HUGE Boy) or small bullets (like Atomizer). This also seems to happen to enemies.
It happens on both challenges and normal runs. I tried.
Also yes it is after a couple runs so I think that's why. Like, I have Atomizer in my last run and the next run I will randomly have small bullets, but then occasionally it will be random and give me HUGE Boy bullets even though I didn't have that upgrade.