I don't think FF13Fix will affect this in any way. This seems like GPU drivers issue.

Thank you for your input

Well, you didn't mentioned one basic thing which is rather important for troubleshooting.

Does this happens all the time, even with unmodified game, or does it only appears with FF13Fix applied?

I had FF13Fix applied to repair UI in 1080p resolution, (the "SetScissorRect" bug) and never encountered such graphical issue.

Also, you never mentioned any HW specs like GPU.
I can only guess from your other videos on YouTube that you are using Intel Arc, and it might be compatibility issue.
I however have absolutely no experience with their GPUs, thus I can't tell for sure.

Yeah, sorry for the late reply. You are correct with the assumption of the A770.

Hardware specs are i7 11700k, Intel Arc A770 16g Acer Predator Bifrost, 32G Corsair Vengeance DDR4 ram (don't remember CL) and a 850w PSU. Temps all around are pretty solid and low with this game.

I honestly couldn't tell you if it would happen without the FF13Fix, as the game would crash VERY frequently without it. I can tell you however, that apparently Arc cards are notorious for running bad on dx9. This is pretty much the only dx9 game I play, but with the FF13Fix and a few adjustments in there, I can run the game at 3840x2160 around 110fps open world and 80-90fps during a battle.

I have grown to just live with it, but I greatly appreciate your willingness to respond and help.

Only thing I could add, is that I've tried to run the game both in UHD resolution and with uncapped frame rate, and none of that caused any sort of graphical glitches for me on my GTX 1060.

The issue might really be in GPU drivers not correctly handle instructions from dx9 rendering for the motion trail in Lightning's gunblade models.
Making the motion trail jump all over the screen instead.

At least that's what it appear to be in the video.