I wanted to try out your theory but... the bug vanished, without any intervention on my side ! I'll keep an eye on it.
It happens for example if you take beam rifle with ninjutsu as secondary.
The sword bugs the rifle animation, in fact if you change swords the shot comes out higher or lower.
For example, take the post apocalyptic pruner which is very long and the shot comes out too high.
Take the ninja sword which is very short and it comes out too low.
This game seems to have issues with powersets with multiple weapons in it.
For example if you take a blaster with dual pistols/arrows, the bow disappears.
The corruptor version is fine though.
So i think it could be a small overlook, easy to fix.