I usually bid within the bid/ask spread, so sometimes my order is partially filled while waiting for another seller to sell me the remaining units. They always show up as a single trade with a single commission, if I let the order complete.
Not sure what happened to yours. Did you modify the order when it was partially filled? Even then, it should still be considered as a single order, unless you cancel it and place another order. Maybe you should check with IBKR directly for an official answer. They have your full order/trade details.
I think I understood what happened. The system filled the smaller lot first for my buy order which incurred the fixed 5 charge. But when it filled the second larger order, the commission was reduced to take into the commission for the first trance such that the total commission is correct.
