I am running the beta on a Macbook Pro 15" Mid 2015 model. I have 2 external displays plugged in to the MBPs two thunderbolt ports.
However on 10.12.1 suddenly only one display works at a time. If I have two plugged in, the first one plugged in will work. The second one will act as though it were not plugged in. If I unplug the first, then the second one will activate.
I switched backed to my partition without the beta and this is not an issue. I have filed a bug with Apple but I wanted to see if anyone else has seen this or similar external display issues.