If the pin holes are only slightly off, you should try installing the pin or pins from the other side of the frame. Sometimes this helps to align the rail inserts.
You can also try to force fit the rails by inserting the supplied drill bit into the frame pin hole with only the rail section installed. Having the drill bit in the drill can provide some mass to push the drill bit in. The taper on the drill bit can align the parts more easily than the taper-less pins. Once the pin is through both sides you can pull the drill bit straight out, which should clean up any edges and flashing that might be holding up the pin.