I posted the same issue over a month ago at the link below but the issue persists
I did what it was suggested that is changing the shortcut for Run Current Line of Command but the issue keeps popping up at random. When the shortcut is set to CTRL + Enter it works for a while but then, without any apparent reason, it switches back to opening the source code. Note that this happens when RStudio is running and not after shutting it down. When this happens, I shut down RStudio and boot it again at which point the shortcut CTRL+ENTER again works again.
The same issue happens even when I set up CTRL+SHIFT+ENTER as shortcut. So I think it may not be related to the specific shortcut but a bug.