In the case of that IST fare the issue was that the lowest base fare was prioritized even though the YQ made it higher in the end. So the higher base fare/lower YQ combo actually was cheaper but ITA (which is the back-end for United.com) didn't list it as the cheapest based on their search algorithm.

Other than that, this sounds like a great opportunity to get a LFG if you can get another engine to price it.