Why would you agree you pay money you don't owe? Their number should be exactly what is shown on your W-2.
If that is not the case, then it is a problem that you need to take to your employer because they aren't remitting it correctly when doing your payroll.
My only other guess is that you forgot to submit your local tax return. I don't think all of the information is being presented here.

As far as Keystone Collections goes, I've heard they are shitty to deal with. I've also heard that about pretty much every organization that exists solely to collect your money.

I've done payroll for numerous companies in PA.