2008 Ford Taurus Motor oil in Transmission

I went to a national chain mechanic to have an oil change done. They informed me that the mechanic messed up and put the motor oil in the transmission - not the engine! They did a transmission flush but said that the filter (in the transmission) was not touched by the oil. I insisted thaat the filter needs to be changed.
Question: who's right regarding the filter change? Are there any other concerns that I should have addressed?
Thanks