Given the number of technological glitches that exist, I do think it's *possible* that she did actually select google checkout and somehow the system went wonky. Or it's possible she *thought* she had, but misclicked. Or who knows. I don't know if those are very likely, but they are possible.
So if this happens in the future, a tweak in phrasing might be helpful, so that you communicate exactly what you need to, but also leave open the possibility that it wasn't actually the buyer's fault. Perhaps something like "Thank you for purchasing Item X! Unfortunately, there seems to have been an error in handling your payment. As the item description indicates, we are only able too accept Google Checkout as payment option. If you attempted to complete your transaction using something other than Google Checkout by mistake, please cancel that payment option and resubmit with Google Checkout. If did use Google Checkout, it should have gone through correctly, so please let me know immediately, so that we can fix the error. Thanks again for your interest in our shop!"
I think the benefit here is that it still points to the item description payment instructions, to prevent 'but I didn't know that!' protestations, but it also avoids any feel of 'scolding' if the buyer did actually do her part correctly, or made a silly error. If it were me, I would find "which is clearly stated on the item description page" somewhat scolding, and it would be irritating to me *IF* I had actually done nothing wrong.
I don't think you were rude, exactly, but I think a shift in approach could be beneficial in some cases. Of course, some people, no matter what you do, will be difficult.