2002 Honda Civic LX Sedan

I have a Civic that iI have 100,000 miles on and decided to get the timing belt replaced along with the water pump and belts. I also had the transmission fluid changed. When I picked up the car after driving two miles the radio went dead and the ABS and SRS along with the engine light came on. All of the gadges would go dead also. When I stopped due to traffic the transmission would not react immediately but would engage, but it would be very jerky.I had them check the bralkes which did not need replacement and had them check the battery out which according to them checked out good. I was very concerned about driving this vehicle back to the dealership, but did the next day. Now they are saying the battery is probably bad or the alternator is bad. Could this have been caused by anything they did? What do you think is the fix?