If you went to dev mode, I assume you’ve already workout out what why both Knots and Core appear as installed, as described here:
Since you’re asking again… maybe the missed the explanation but found the steps to switch from one to another? And guidance you found that tells you to go to dev mode will have explained why both appear as installed and that it’s OK.
I don’t know what you mean by installing “by hand” or via “manual code”. Perhaps installing via sideloading the sp9k file? How old that original (possibly unsupported at the time) file might affect things during an upgrade, I can’t be sure, but your specific error is something I’ve only seen when someone switches back and forth between Core and Knots in rapid succession. Do you think you might have done that?
It this point, the fastest way out of this situation is to uninstall either Bitcoin Core or Bitcoin Knots… then make a firm decision as to which you want, then install that. From that point on, only upgrade the one you have.