I brought my 2012 Focus in at 8A.M. for two recall...

I brought my 2012 Focus in at 8A.M. for two recalls(something with the wiper motor and a computer upgrade for the transmision shifts), and a Mass. state inspection. I was told it would take about two hours and they would call me whe it was ready. At 1:30 P.M. I called the dealer and was told the car was being test driven to make sure the car was shifting correctly and after the test drive the inspection would be preformed. I was then told the car would be ready by 3P.M and they would call me when it was ready. I hadn't received a call by 3 so I went to the shop. The service rep told me that the emissions memory on the computer got erased when they upgraded the computer so the car failed the emissions part of the inspection. he also told me that they took the car on a long drive to attempt to get some emissions data into the computer so the car would pass.
I do not like the fact that I wasn't told when i called at1:30 that there was a problem and I am disapointed to find out that whomever scheduled the order that the work was to be preformed in did not realize that the emissions test should be preformed BEFORE the computer is touched.