Means you installed something from outside of the package manager somehow … a script, a driver from a website, etc.
This may have been part of your original problem.
There are a number of ways to remedy this, including removing those files first … but I do wonder what other paths may have been superseded by some sort of unsupported install.
(another approach would be another overwrite sudo pacman -Syu xf86-video-intel xf86-video-nouveau lib32-vulkan-intel --overwrite '/usr/*')
I suppose you Can just go forward dealing with these conflicts as they arise, but it would probably be best to figure out what was done in the first place so it can be thoroughly undone.
What @scotty65 says is also true, if not the direct issue right now.
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