I don't know if there are any situations where they both make clear predictions that contradict each other, but see
here for a discussion of one of the main problems in figuring out how to reconcile them, having to do with the fact that the uncertainty principle would seem to allow for huge uncertainty in energy at sufficiently small scales, but in GR big energies cause significant curvature of spacetime, and my understanding is that physicists only know how to make predictions in quantum field theory if they have a specific known background spacetime.
I guess another more general conflict is that quantum field theories treat the other set of forces using a common set of rules, but if you try to apply these rules to gravity you get infinities which can't be "renormalized" as in the case of the other forces.