Any reason an ECM computer can fry?

I recently took my 94 Honda Passport to a local shop for a clutch inspection, I was told that in order for them to inspect it they had to remove the transmission. Later come to find out I needed a clutch set, flywheel,etc... the service manager called me back to inform me he had good new and bad news, First, the good new was that the radiator had not been leaking coolant, second, the clutch set was placed in the car the technician that worked on the car took it out for a test drive and it ran beautifully, However, when the technician shut the car off and attempted to start it up it would not start. Service manager said engine would not crank and there was no spark, it must be an electrical problem he said. Diagnostic determined ECM computer had been fried. I told them to leave my car alone and I would find a way to get it out of their shop. Service manager called back w/in 30 min advising me he spoke to his boss and they would give me the computer discounted and I told him I should not have to pay for all I know the technician that worked on my car could have possibly fried the computer. They would not own up to their mistake that cost me more money so I ended up paying almost $400 just because it was going to be 4th of July weekend and did not want my vehicle sitting in their shop any longer plus I need transportation for work. Can anyone please give me advice? Could it be possible that the technician when placing the transmission back into the vehicle could have fried the ECM computer? how do ECM computers fry? How can I prove in small claims court that my car was running properly when I left it in the shop's possession?