The Gambas IDE is possibly not as sophisticated as some other IDE's. You need to set some breakpoints before you run your project if you want to use breakpoints.
When your project is running, you can only toggle breakpoints in the code editor when you are at a breakpoint in the code editor. Yes this is a restriction. It does mean if you have no breakpoints you will have to stop your running and then add some.
This is not really a bug, so much as a not very sophisticated debugger.
Also the tree in the hierarchy does not collapse. Again not a bug. Just the lack of a feature.
Not sure I am really worried about either issue. I think there are more important additions that should be added to Gambas first.