Without wishing to be argumentative, what is there to suggest the problem is not just an issue with 93001? Given there is only one on the Network at the moment, there's no indication of that. As for 93002 - I havent been told that it has been accepted or passed for operation under its own power on the network ( I could have been and I havent been informed! ) but if it hasnt, thats why that didnt go to Crewe to replace. There's much discussion within the rail freight industry of the locos, little of it seems to be good, but the vast majority is speculation and rumour.
The one thing for sure is that while a Class 93 is around 20% of an '88' in terms of components and parts, it is a very different machine, and "very complicated". But its also new and teething problems, minor issues and quirks all have to be worked out with everything that is new.