That did not change anything, here is an example video of distortion and stretching issues https://i.gyazo.com/e74ec0ee9fa6bc54301d54638299d9f3.mp4
There are a lot of vertices that are not being matched (15 in this case) that unfortunately contain some of the most important movement information
I always end up having to redo any existing shapekeys

Crowbar, "Version 0.58" to export them (with SFM and GMod decompilers)
Blender Source Tools (for Blender 2.8 (this happened on earlier 2.79 versions as well)) (latest version)

I could do this for every model from sfmlabs or garrys mod addons or sfm addons, it occurs with each and every one so there is no 'one reproducable model' because all of them fail.

No, the problem is it can NOT 'just be deleted' because the unmatched data is crucial to most of the flexes, meaning some vertices on the face or eyes for example will remain stagnant throughout all my shape keys creating weird distortions and unwanted stretching

Ive never been able to import vta flexes appropriately from crowbar into blender, Ive tried with SFM and GMod decompilers but both of them end up creating these 'unmatched vta vertices' which will ruin every existing shape key as some shapes for verts of the face or eyes and such will not exist