I do not know how to fix the problem, but I can give some more information.

This seems to be an problem with Crowbar decompiling and not with BST importing. Crowbar should be decompiling the animation data correctly; the "taun01" sequence was probably created as a delta sequence somehow.

The "taun01" sequence is blended with the "layer_taunt01" sequence. The "layer_taunt01" imported into Blender shows the expected taunt animation.

I do not know how the "taunt01" was originally created or why there are two sequences blended together to make the one animation.

Maybe the $upaxis Y option in the QC is the distinguishing factor. I noticed the Scout model had it and it was messed up via QC import.

If you decompiled with latest Crowbar 0.66, then try to decompile with Crowbar 0.65. There is a bug with 0.66 that I plan to correct today.

Materials and textures are totally separate files from the model files. Learn how to work with Source engine model textures: https://sites.google.com/site/zeqmacaw/tutorials/troubleshooting-missing-texture

Using Blender 2.80.75 with BST 3.0.2, I get the same error.
Using Blender 2.79 with BST 2.10.12, the VTA loads correctly.

The image shows what appears to be the lod1 mesh, which might not be the main reference mesh. The VTA only works with what is typically the reference mesh or lod0.

I encountered the same issue and error message as reported in original post.

Linked is a 7z file of 4 files where I saw the issue: import VTA in Blender 2.80.7z[drive.google.com]

Steps taken using Blender 2.79b with Blender Source Tools 2.10.12 that import the shape keys correctly:

Steps taken using Blender 2.80 (whatever Steam is using) with Blender Source Tools 3.0 that show one importing correctly and one importing without any shape keys beyond "basis":

It is not helpful to tell me there are problems without telling what models had problems.

You can check if it is Crowbar messing up by decompiling the original model then compiling with no changes.

Proportion Trick[sites.google.com]