Have you tried "sfc /scannow"?
@XhenEd I have seen this work wonders for some systems.
I'd also recommend reading this:
How to use DISM command-line utility to repair a Windows 10 image
If for some reason sfc /scannow does not do the trick (meaning you have executed this command oh let's say three times) I would go for DISM.
First, I would run this to check: DISM /Online /Cleanup-Image /ScanHealth
Second, if anything is amiss I would run this: DISM /Online /Cleanup-Image /RestoreHealth
For another great measure (if your Windows is on the "C" drive) I'd run a check disk /f. What to run: chkdsk /f c:
**Notice*** I am using /f NOT /r. If you use /r it may take hours or days to repair stuff. /f usually should take between 10-20 minutes depending on how large your hard drive is or the "C" drive is. The smaller the faster this will run the larger the longer this may take. My 2TB hard drive takes about 10-15 minutes while a 500 GB hard drive may take 5-10 minutes, but it depends on what may be going on with the HDD as well. SSDs, on the other hand, may not benefit much if anything from a check disk. However, a /f does help with filesystem errors and this will help out if there are filesystem errors.
From there you would have to input "y" if you agree to restart your computer now to run the check disk or "n" if you want to restart later. I'd personally do "y" right then and there if possible.
If you want to get all fancy you could then type in: shutdown /r /t 0. What this command does is restart your computer with a time frame of 0 seconds. Or a quick restart right then and there without having to navigate over to the restart.
Keep us in the loop on how everything goes. I do agree with what XhenEd suggested - try out the sfc /scanow option and see how that goes first. From there move on to DISM with the /Scanhealth option and on to /RestoreHealth option if there are problems found. A good ol' check disk never hurts either. Just remember to do a /f and all will be good.