Thanks for your answer.
I'm facing this issue with many apps, even stock ones. For example, System Preferences, Activity Monitor, etc.
I'll try restarting my system, but I've faced the issue a few times and I've already restarted during this period so this isn't a great fix.
I'll try updating to 10.14.2 and see if it changes something.
I also think that this issue was related, because I don't think the OP was talking of minimized apps.
And yes, I know about your note, and I'm only trying to switch to apps with an already-opened window. And in my case, the menubar doesn't change at all when this bug occurs.
EDIT : I've just updated to 10.14.2 (and so rebooted my machine) and bug is still happening.