In my experience with a similar fault on a 1.8TDCi C-Max, Ford dealers have no idea when it comes to intermittent electrical faults.
My car started hesitating, cutting out and displaying 'Engine System Fault" just out of the warranty period. The dealer diagnosed a crankcase sensor, which they replaced at a cost of £250. I drove it home and it cut out again. Got them to try it again, and they had to get a Ford specialist technician in to look at the car, and he suggested it was the wiring loom.
The problem went away when they fiddled with the wiring loom, though it's ocurred a few times since, normally in very damp conditions, so I reckon there's a dodgy connection somewhere.
With your car being in warranty they've got no excuse. Get them to sort it out once and for all. If necessary insist on a courtesy car while they fix it, and ask them to get one of the specialist technicians from Ford to take a look at it, because dealers really don't have a clue in these circumstances.
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