I do sell stuff for Bitcoin. Usually it works normal. But quite often I see buyers who order product but send less amount. It seems Bitcoin fee was deducted from that amount. Obviously merchant script does not trigger and waits for more bitcoins to arrive.
Consider making your merchant script more 'smart'! Despite the inability (and sometimes intention) of customers to send proper payments, you should think of how much is missing (total percentage) and is it worth the hassle with the delayed and pending order.
Compare it e.g. to bastards from hell PayPal. They deduct a noticeable percentage as fee. If the percentage you miss is below that, don't care and swallow it. At least with Bitcoins noone can freeze your account or charge back the payment. That alone is worth it over fu***** PayPal.