Have you asked your customers?  It would be a good thing to know and they likely are the only ones who are going to know for sure.

It's likely they're withdrawing from an exchange or other e-wallet that has a withdrawal fee in addition to the transaction fee. People need to either 1) stop using goddamn sites that charge withdrawal fees or 2) overbuy BTC on exchanges with withdrawal fees, withdraw to their personal wallet, then send from there, using the appropriate TX fee.

I am fairly certain no desktop client deducts miner fees from the amount sent.  MtGox charges 10x the min fee for withdraws but it is taken from account balance not the amount sent.  I am fairly certain bitstamp and coinbase do the same.    So it probably is some web wallet or smaller exchange.  Not sure why people use exchange accounts as a spending wallet but they do.    I agree with the OP it is an utterly stupid decision.  I mean it break even "common sense".  If I use my bank account to do a transfer, bill pay, or even bank wire there may be a fee but the fee is never deducted from the amount being sent.  It would cause all kinds unnecessary chaos, support calls, and upset customers in the traditional finance world as well.

If any user (or any service, exchange, web-wallet, etc) can confirm an instance where a tx fee, or withdraw fee was deducted from the amount sent please post an example as someone needs to beat that developer over the head with a book on software design.

just-dice

Maybe they're using some mixer to be anonymous and aren't taking the fee into account.

Just today I got contact and chased one of the buyer with BTC transferred incomplete. He said he used BTC-e for payment.

Unless we take care of these small issues, BTC will never get popular with online merchants.

BTC-e clearly states how much is fee and how much is actually transferred.

Simple user error.

I'm not sure if you are familiar with the BTC-e withdraw form. It says "You will receive:". That's the amount the entered address will receive. If the amount in there is not the amount that the address is supposed to receive, well, then the amount was entered incorrectly. I think some things can be expected of the user.

Leave out the transfer fee deduction and you have users complaining of being ripped off.

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.