I think that it's reprehensible to charge someone more than quoted for shipping. I understand that they're having a problem with their shipper, but again... THEY'RE having problems with their shipper...

I would ask them to refund the difference from what you were quoted to what was charged. Why should you pay for their problems? What if you only HAD $100 in your acct when they decided to charge you $121? You'd have an overdraft fee and had to pay a penalty to your bank for THEIR charging you more than you agreed!