Yep, I have the exact same problem. Haven’t had much time to troubleshoot but it seems that certain buttons aren’t mappable from the GUI with AdvanceMAME. The ones it does map it gives weird names like “top” for the start button or “trigger” for the select button. Basically exactly what the OP posted.
It also seems to inadvertently pick up inputs from the PS3 controller’s motion sensors and tries to map them as axis.
Using PS3 controller over bluetooth. All other emulators work fine.
Pi2 and RetroPie 3.0 beta 2.