Unreacted body filler contains styrene, which until fully catalyzed acts as a solvent that can penetrate materials that aren't solvent resistant. 2K urethane primers are somewhat solvent resistant, but this resistance develops over time, and even then the primer remains porous and subject to chemical attack. That's why 2K urethane is never suitable for a topcoat.
Sometimes it happens that filler needs to be placed over 2K urethane primer. The procedure that I recommend is to first make sure the primer is as cured as possible, with the maximum amount of heat and time that can be managed in the repair area. Second, use a heat source to cure the filler and to either cure or otherwise drive any unreacted styrene out of the primer. 120° for at least a half hour depending on the thickness of the fill.
After that, the area should still be given extra time and heat during priming stages, since it should be suspected that some solvent remains under the filler. As long as heat and time are used to make sure solvent is out from under the repair, there is a high chance of success.