Player/faction discounts are applied twice when buying/trading. Once when confirming the purchase in trade window and then again when the trade is executed (i.e. you get some money back). (observe by using one trader only and compare trade amount in window vs player account balance variation post transaction)
Function execute_trade in aiscript order.trade.perform seems to be the culprit, though not sure how it is envolved in the profit prediction further below.
Below is a sequence of small screen captures, showing the account variation:
And associated incorrect profit prediction from sales:
