Only if the warnings come up too often. I imagine it should be quite possible to define criteria that discriminate selling shares at a price of 0.0000016 yen from normal prices, by comparing with the market price, or the range of prices ever seen by the software, for example.

Alarm fatigue is an important design consideration, but not a reason to not put warnings at all (given that this isn't amenable to an "Undo" button, which is preferable when possible).

Alarm fatigue is indeed an issue -- but if the trader is repeatedly trying to sell for way below market price that often, then perhaps there is a much bigger problem...with the trader.