There are two simple, repeatable ways to stop the charge attack bullet, both of which have been half-fixed.
The first, as Draycos has pointed out, is to shield-cancel it.
The second, is to attack asap, and thus cancel it.

In my testing, I have done continuous charge attacks, releasing the attack button only for the short period to initiate a charge attack, and have gotten weird results. Without changing direction, moving, or deviating (much) in my regularity of charge attack spammage, most of the time I'd get a bullet, but sometimes I wouldn't.

There seemed to be a higher chance of cancellation when moving before using the charge attack, but I'm not sure. There's probably some pattern to it (not RNG), but the pattern is so odd and quirky that it'd be not practical to learn how to get around this problem. (If it's actually RNG and OOO put this in to troll people like me... q.q)

asdfasdf too lazy to finish my post, if I had not finished it already. I got sidetracked by writing another post .-.

TL;DR Winmillion charge bullet cancel is derpy.