I think the problem may have came from an fsck.
Yessterday (around the time this problem showed up), while booting it did an fsck (mounted 25 times with no check) and it had some errors.
It booted me into a recovery shell to correct some errors.
There were several problems with various things, so I'm wondering if I answered something incorrectly.
I honestly just answered 'y' to everything because I didn't have time to waste and really needed to get my computer booted so I could get to work.
In my case /etc/alternatives/xinput-all_ALL is an exectuable, which I'm not sure if thats correct.
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