It was something that Arcturus didn't really know, but according to the information that he passed to the Grandmaster Byrmellir, there was a slight possibility that the Greenskins would cooperate with the Mind Flayers.
While the possibility for such cooperation was low, it still existed and represented the danger for the entire Frontier Star Segment because together, they would be much harder foes to deal with.
The Imperium wouldn't have to deal with just the Mind Flayers and their advanced and esoteric technology but also with the sheer number of the Greenskins that would be coming at them in hooves.
If the Greenskins and Mind Flayers joined and coordinated their attacks together, it would spell a literal catastrophe for the entire Frontier Star Segment because both sides would perfectly complement each other.