You may have produced a design that requires multiple different parts to be fit to a single reference designator. This is quite common when using modules attached by connectors such as the Arduino.
We would argue this is bad practice as a reference designator should denote a single fit. The CircuitHub BOM tool does not allow you change the BOM generated by your EDA tool as we believe your EDA tool should be the source of truth. We would recommend you change the underlying EDA data but if you want to avoid doing this, you can go ahead and place the order and make a note of the changes required as an issue on your order page. You will then be billed for any additional component purchasing required.