Some shortcuts are currently defined two times. One time in the scriptDockWidget and one time in the mainWindow. Examples are Ctrl+O (File Open), Ctrl+N (New File), and all the Python Debugging Shortcuts. Depending on the current shortcut context, either the shortcut is only executed if no script editor is currently docked in (Ctrl+O, Ctrl+N) or it is only executed if the script editor has the focus (Python debugging actions).
The reason is a Qt warning: ambiguous shortcut overload
Possible fix: Probably the only way to fix this will be that these actions are only generated one time as global, application wide shortcut, and are then re-used by the main window as well as the script editors.