You don't need large scale fraud, you only need to defraud key population centers in a state. Think of how the electoral college works, you have districts broken up geographically and weighted by relative population. Take my state of New York for instance, this place is a solid lock for Hillary but most people don't realize how red it is; because of the overwhelming number of people in NYC we always come up blue in the polls. There are literally millions of people elsewhere in the state that are die hard republicans. Now assume that those people are going to vote red and their district is going to come up for Trump with no need for manipulation. You wouldn't need more than a handful of compromised machines in Buffalo, Rochester and\or NYC to alter a few key districts and flip the entire state for the republican party for the first time since the 80's. People would ask questions sure, but by then you could easily have the few dozen machines you compromised flashed back to their stock firmware, or destroyed in a fire or what ever the hell you wanted. There are enough people who would have actually voted republican who would jump at the chance to defend the results on national television and insert that feeling of reasonable doubt.
You're mistake is in assuming that just because candidates win entire states at a time, that those people in those states must all vote the same way. This is completely incorrect.