Cause of corrupt system files?

Certain programs can make changes to system files, from permissions to modifying their resources (icons etc). These changes can result in such discrepancies.

In the last month or so, a minor bug was introduced by MS where an issue with Defender meant SFC reported corruption (details are available on this forum e.g.) - not the first such MS-added discrepancy.
MS Posts Support Note About Defender SFC /Scannow Errors

Finally, things could potentially be overwritten or become corrupt- e,.g. HDD failure.

It is worth monitoring your disks- Hard Disk Sentinel (paid) e.g. allows threshold triggered reporting.
And routine disk imaging intrinsically verifies the integrity of the used parts of imaged partitions.

Win20Win said:

I've been in the process of removing data from a Win 10 machine for several weeks now, during which time it has not been connected to the internet, and no new programs have been installed on it. However, today, when I was trying to run malware checks on the appdata folder, the anti-malware package that I have installed on the machine began struggling to initiate scans, or completing them instantaneously, or other bugged behaviour. ...[SNIP]...
My question is this: on a machine that has not been connected to the internet or had any programs installed on it for weeks, how is it possible for some of the system files suddenly go from uncorrupted to corrupted?

Hi Win20Win,
Dalchina has pretty much answered your questions, but I'd thought I'd add just a little bit...

Win20Win said:

Could I have triggered some latent malware on the system by poking around?

Yes, it is possible, but for SFC /SCANNOW to "fix" things, highly unlikely is was an infection.

Win20Win said:

Could it be the bizarre (and very brief) 'update' that Windows did a couple of days ago even though it can't have had any updates due to not being connected to the internet?

How could the computer have updated if it was not connected to the internet? Did you update it manually? Is it on a LAN and possibly got the update from another computer on the same LAN?

Win20Win said:

Perhaps some conflict between the two anti-viruses? I'm hoping someone can offer an explanation as right now I'm fretting about the malware option.

Possibly, but unlikely. You never mentioned which 3rd-party AV you were using.

There are infections which are "time bombs", in that they have a delay before deploying their payload, but it doesn't sound like that's what happened to you.

Sorry I can't be of more help.

This is what I was wondering. It was a very strange occurrence: When I shut the machine down, it unexpectedly went to the standard 'don't turn off the power b/c updating' screen

That, of course, should only occur if there's a pending update which has not been completed; you would normally expect to see an 'update and restart' option if so, for example, if using a menu option to shut down.

If you had not done a full restart or shut down for some time, but hibernated, e.g. then yes, an update could be pending for quite some time.

Potentially malware could be written to behave in any way at any time... if you were detecting malware, or had reason to run scans, then the unpredictable becomes more likely.

I've added a link referring to the SFC / Defender issue above.

You could run
chkdsk c: /scan
from an admin command or Powershell prompt - this checks file system integrity, no repair.

Have a look at your Update History (Settings, Windows Update - or search) and check the record for failures.
The News section here has a thread per update per build.