The Seraphims are probably programmed to obey Marines, and Vegapunk is the only one with total authority over them, so if he ever decides to betray them, he could essentially take away a huge chunk of their power.
Also, it could turn out he has been a secret Revolutionary all along, and they found out. If that's the case, he could be plotting to turn the Seraphims on them.
It could be a multitude of reasons. I doubt it's going to be something inconsequential or insignificant. Or at least I hope not.
