Karugul is a phase boss. This means that once they take enough damage, they will move further into the lost sector. 
When looking at the area with the black squares on the floor in the first room, a subtle effect is put over the lighted surfaces that uses the player's position as a reference. The effect is that of light reflecting off of water, and it changes based off of the viewer's movements. 
There are small pulsating orange sacs to the right and left of the lost sector chest that rattle back and forth when shot. 
There is a very large, slowly moving, tentacle behind the lost sector chest of unknown origin or species.