ECM failed

I was grocery shopping, went to get in my car and it would not start. Lights, windows, radio all working. The push start button allowed me to go from off to aces and then to start but the vehicle would not start. Had the vehicle towed to the the dealer. It has been there for seven days. Yesterday they called and said they did not have an update. The dealer called today and told me that the ECM is bad and the battery is dead and failure is due to a cross jump. He said that they put an ECM and battery from another Santa Fe and it started. I explained to them that the vehicle just would not start, and I did not attempt to jump as I did not think it was a battery issue as I still had power when it left on the truck. He mentioned that Hyundai said because of the failure reason they will not cover the repairs under warranty. I have an extended warranty too, they said it needed to be handled through Hyundai. I wonder why they did not even ask me if I attempted a jump? And the battery was not dead last time I was in the vehicle. Should there be some sort of evidence that it was cross jumped for them to make that assumption?