The apps should work great together. It just sounds to me like you setup competing configurations which you didn’t intend. Let me know exactly what you configured for each of the buttons in Button Controller Plus as well as “Automate Lights & Switches”. Maybe I can help you figure out what you got going on. Maybe you found a bug in the smartapp?
FYI: it is always a good practice to post your question about a custom smartapp in the thread on the smartapp itself. That is the one that the author and other users with questions or issues typically monitors. Someone with your same issue might not be seeing it here. 