If you mean real time PCR, then make sure you piped the exact same volume of everything for your duplicate wells, and make sure you really seal the wells very well if you use membrane in stead of the clear flat caps.
Verify that your pipettes are working properly, that multi channel pipettes are consistent between channels, that you equilibrate your tips with whatever you are pipetting by wetting the tip. Verify your technique. The smaller the volumes, the more careful you need to be.