As mentioned above, PE is made using a chemical "milling" (etching) process. The discolorations on PE sets are typically either residue left behind from incomplete post-etching neutralization and cleaning processes, or tarnishing and surface oxidation - which may result from pre-packaging handling, etc.
Unless the "blem" is an oil, it is unlikely to affect either part stability and longevity in your build (i.e., it won't corrode away) or affect your painting.
To be safe, I always inspect PE sets and wash them in soap water with attention to the blems. Washing will remove oils left from processing and handling and generally remove any possible acid residues left from etching. If the blem has some marked surface texture that you don't want coming through your paint... do a light sanding with very fine grit paper to smooth and burnish the PE sheet before cutting parts off.
Cheers! Bob