New GAF roof installed has color differences due to oil staining

[Gail A Newton]

New roof installed this weekend by a roofer with GAF shingles.  It looks like they used two colors in some areas.  Very obvious - neighbors have even commented on it.  The Roofer and GAF territory manager say it is due to "oil staining" and will blend in 60-90 days.  If it doesn't, they will help me file a claim.  This makes me nervous.  I haven't paid yet.  Do I pay in full?  I feel like I shouldn't have to pay the full amount until the roof looks like it should look.  Anybody ever had this experience before?  Thanks so much for your help!