This happened to me, as I was on the final part of Cass' questline where you either find evidence of Van Graff and AM's conspiracy against the caravans or you kill Gloria, John-Baptiste and AM.
While doing this I was also on Van Graff's questline, and John-Baptiste had told me to bring Cass to him so they could have a talk, however even though the quest marker pointed directly to Cass (which was following me) she didn't have any conversation options to talk about this whatsoever since I'd already recruited her.
When I brought her to Van Graff, he of course say he's going to massacre her and initiates combat. Me, Cass and ED-E finish them all of, and Cass then immediately tells me I'm [censored] for telling her I was going to get evidence against them and then murdered them instead... Wtf?
I reloaded a much earlier save, where Cass was still my follower, but I was on the part of the questline where you stand guard in front of the Van Graff building, this time: I let the "terrorist" caravaneer into the building and he blew the whole [censored] sky high. Cass immediately runs up to me and tells me why we're gathering evidence against them if I was just going to murder them anyway... Wtf again.
You can however gather all the evidence, turn it into Jackson and get a nice peaceful complete that way, but you will never be able to finish the Van Graff questline and if you've already started it, it will be stuck in your questlog forever.
Because of this I had to reload way back to a save where I'd not started the Van Graff questline. Which is ~12 hours of gameplay, suffice it to say I'm sad I have to redo three days worth of playing because the game is bugged :/
TL;DR Don't start the Van Graff questline if you ever plan on finishing Cass' companion mission the peaceful way.