Macintosh HD Storage Incorrectly Reading as Full, Which is Causing Problems

The affected device is a 2020 MacBook Air with 994.66 GB of storage on its HD. It's running on the Sonoma 14.3.1 macOS as of one/two weeks ago.

Over the last few months, I've been using MovPilot and NordVPN to download my favorite movies and shows as mp4 files after getting frustrated with how they jumped from one streaming service to another, especially if they were services I didn't have accounts with/access to. I quickly realized that this was taking up a lot of space on my laptop, so I purchased a 5 TB external drive, moved everything that I had already downloaded onto there, and deleted the originals from the hard drive. After I emptied the trash, the hard drive storage cleared up by quite a bit.

Since then, my process has consisted of downloading content onto my desktop, copying it to the external drive, and deleting the original from the hard drive immediately after. It's worked out well for months and I have now used up 934.45 GB of the external drive's storage.

Today, however, I was unable to complete a download due to insufficient storage space on my hard drive. This surprised me because I was supposed to have several hundred GB left. I opened System Settings and saw this:

First of all, I have nowhere near that many applications. I took the trouble of adding up the GB, MB, and KB of each app, and I didn't even hit 25 GB. But according to System Settings, I have 432.95 GB worth of applications. I have no idea where that number is coming from, especially since clicking the information button (the "i" with a circle around it) shows this list of applications, ranked according to size:

Second, iCloud Drive is also inflated, at 473.35 GB. My iCloud Drive is composed of my desktop, my documents, and my downloads. Those three add up to less than 100 GB, which is nowhere close to around 475 GB. Don't even get me started on my documents. I have no idea how 2.7 MB is over 40 GB on System Settings, and clicking that information button was another exercise in futility.

I went to the iCloud section of System Settings and the iCloud website, and got the following values:

The drive is less than 100 GB. Not nearing 475 GB. Also, my photos are 286.2 GB, not the 321.28 GB that System Settings is telling me. (This may be a stupid question, but if the desktop, documents, downloads, and photos are all on the iCloud, then why are they taking up any space at all on the Macintosh HD? Is it because I haven't optimized anything?)

Over the last six hours or so, I've disconnected and ejected the external drive from my laptop, thrown a bunch of items in my trash and emptied it, and restarted my laptop twice. No dice. I've even run Disk Utility. It doesn't see anything wrong. The storage on System Settings is all haywire and I'm now getting a warning that my desktop may be out of date. Also, this is going on now:

I genuinely don't know what is going on here or why. But if anyone has any idea, please, let me know.