Former title: SSD having issues after I filled up its storage

I wrote this poorly last time so here's a more clear description: Hey all, so I filled my SSD up on Linux Mint and it's running sluggishly. I deleted more than half of my storage but there's still issues. It can read / write fast according to my inexperienced testing and I have trimmed it (to my knowledge) but there's still issues. Loading up programs now takes 30 seconds (even something like VLC which typically took like 0.5 seconds). Loading new audio files into VLC can take 10 seconds. I have checked my system monitor and nothing seems out of place. Also, when the program starts running, it runs perfectly. The computer itself is fast but loading anything new takes ages. Does anyone have any ideas? It's a new laptop, not even two months old.

Edit: This is somehow, and strangely, a Flatpak issue apparently? It was triggered either by a full SSD or the new Linux Mint 21.3 Cinnamon update.

Edit 2: Interesting experiment result

'it took 30 seconds but this got outputted and then the file ran: dave@dog: ~$ flatpak run org.x.Warpinator Gtx-Message: 14:29:03.389: Failed to load module "xapp-gtk3-module" Using landlock for incoming file isolation'

It appears there's either a xdg-desktop-portal-gtk and/or xdg-desktop-portal-gnome error and I'm not alone, Mint and Arch users are both reporting it as of recent strangely???

This was a real sneaky fu(ker as it dodged all logical system testing. The only reason I caught it was cause it was suspicious how fast system programs booted and how flatpaks booted like sh(t. Not sure if I'm even right about the module, but I'm highly suspicious

Some comment mentioned this and it explained it well: Random shot, because it's probably not an issue on Mint like it was on Arch a few months ago, but xdg-desktop-portal problems can cause apps to take forever to load, but run fine once loaded.

edit: Try removing xdg-desktop-portal-gtk and/or xdg-desktop-portal-gnome