Contamination

DNA can easily aerosolize, contaminating reagents, plastic ware, and DNA samples. This contamination leads to problems with band(s) of expected size amplifying from samples they should not amplify from. For example a wild type band amplifying from a homozygous mutant. This is why including a no template control is so important to include, because it can detect DNA contamination and prevent you from make incorrect conclusions about the genotype of your mice.

If you are amplifying bands of expected sizes in the no template control and samples….

If you are amplifying no band in the no template control, but are in your samples, it is likely the DNAs are contaminated.