I have the same problem, I guess there should be any way to it because is very common to have several layers in the same point and you should be able to choose which one you want to process.
I've been trying really difficult things to trick this behavior. At the end looking for new functions that weren't in the documentation I found it: MVMapView.enableMultiThemeClickable(boolean). They should update the documentation because there are a lot of functions implemented that aren't there.
You just need to enable it and it will work fine!