I also have noticed this, but honestly wasn't sure if it was a bug or not.
I think the ability isn't intended to be used on a planet you are actively bombarding and subduing. The Marauder is a hit and run ship, so I believe the ability is naturally meant to be used as a quick jump in, cast, and jump out. Not as a invasion tool.
If it is working as intended, the obvious solution is to take it off auto cast and use with discretion.