Yes. Mystique in Fractions run when she said she's not stupid enough to be on a team with her and helping Dazzler get her revenge. She doesn't trust her at all. She did with Juggernaut in Gen X after switching is brain off and then again in I guess in the Uncanny Fear itself crossover.
She has with Mojo, in Claremont 00's run. She does something horrible to Mojo off panel and you don't see him for at least 5 years. They leave his fate to Emma in that issue.