The one on the base? Yeah, that's supposed to be there. One of the Klingons is an Undine infiltrator, who then beams back to his ship (the Dreadnought), which is then destroyed by you and the Klingons.
This is mostly FX, but depending upon your settings, some things you need to see show up and some things you need to see don't, leaving you scratching your head. Champions Online is the same way. The game coding is weird like that.