NVME storage not freeing up

I added this NVME drive as my boot disc about a year ago. I didn't realize until last night that there's been an issue with my storage not freeing up.

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I added pictures where you can see I have a backup drive that I cloned from today and that shows the correct amount of storage that should be remaining. Both the NVME and this backup drive are 1tb so they should be close.

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Both the NVME drive and the external USB HDD are using APFS as its filesystem. The machine is an i7-8770k Z370 Aorus Gaming 7 and the drive in question is a Western Digital Black NVME. The hackintosh is running Clover.

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I tried doing some research where I saw rebooting into safe mode could fix it, it didn't. Also, I tried booting off of my backup drive to run First Aid on the NVME boot disc, but that came back with no errors nor did it free up the space. CleanMyMac had no luck either.

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The only thing I can think to do at this moment is to wipe the drive and clone the backup back over to the NVME, but I'm assuming that would only just buy me time as this runaway issue will probably just keep going.

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If there is anyone who could shed some light on this issue, I would greatly appreciated it. Please let me know what additional information I may need to provide.