I'm a sales tax accountant (CPA) in Arizona.
Could be a couple of things.... they can't because their software doesn't handle tax credits well. Since they collect and remit to thousands of tax authorities across the US, credits would have to be claimed from the different taxing jurisdictions. Once remitted, it's much harder to get back. The other possibility is that it really is a government excise tax labeled as a sales tax on the bill, not readily refundable.
All in all, what they are doing is technically legal... as long as they don't file those refund claims and keep the excess funds for themselves. : )