I don't know if I'm the first to discover this, but I tested a bit and compiled the steps in a straight to the point video:

How-to: 0) Do the chaingun ammo glitch

1. Fully charge the chaingun
2. Stagger the boss before they can shoot you
3. Don't let the trigger go nor go in melee range

It works with Arachnids too, I forgot to include them in the video. It also works with normal enemies, although its use is situational (since they will die quickly).