Perhaps the way you mated is slightly different from the way it was modeled.
Can you post a pic or the parts?
Are you able to check the interference between the faces with the Measure tool?
Which SW tool/utility is detecting the interference? Doe it have an option to detect coincident faces as interfering?
I'm using the Interference Detection tool from the Evaluate Toolbar. I do not have "Treat coincidence as interference" checked. It also detects the interference in the Simulation package, which is why it is important to remove the interference.