Looks like your installation got hosed, for some reason. Not too hard to re-install. I found it is no problem to move the Mathematica folder from inside the ~/Library folder, then put back any custom stuff you might have. You can even restore the Licensing folder from within ~/Library/Mathematica so you don't need to re-activate. It sounds like more work than it is. I usually keep the old Mathematica folder around for a while in case I missed something such as stylesheets or packages.
I have had to do this a couple times for various reasons, and you will get back the program in a known state.
In older versions of macOS, there was a similar Mathematica folder inside /Library. This would let any user use the files to run Mathematica. With some OS update, developers (including trusted ones like Wolfram and even Apple) were not permitted to put anything in the root library, so only the user library is active. There is an outside chance that your installation might be trying to use an old Mathematica folder in the root library. No harm in looking to make sure that there is no Mathematica folder in /Library.
Just replacing the app by itself usually doesn't work. If you don't have any custom style-sheets or packages (or similar things), it may be just as well to let Mathematica rebuild the folder and contents when you restart with a new copy of the program. You will need to activate the program from your user portal.
There are pages on the Wolfram site that covers deleting the Mathematica folder. It essentially tells you the same thing, except that it thinks that there are still two locations where the Mathematica folder is. It also refers to two new folders in the user library: Wolfram and Caches/Wolfram. These are new since I last had to rebuild. On my system, there is no Wolfram file in the Caches folder, so either this is not really used, or I never did anything to force the folder to be created. There is a folder named Wolfram in ~/Library. It hasn't been updated since February, so I am not sure what it does. I'll have to remember to teach this when I need to return to a default state. There is also a Wolfram Research folder, but it seems to be involved with the download manager, and in my system, it only has information about versions 11.1 and 11.2. These could be related to a beta test I was involved in, especially since there is no reference to 11.3, where the download manager finally escaped beta on macOS.
How to reset Mathematica to a default set-up
good luck.