What software are you using?
As implied earlier (I think), one needs to be careful mirroring something on the PCB, as that may put it on an opposite layer (i.e, top to bottom). The schematic is much more of a "drawing" program with no top or bottom surfaces, and I have never had a problem mirroring on the schematic using Eagle.
It might help if you could post a snippet of the problem area and tell us the part number.
John