Study this line from the log:

ERROR: c:\users\owner\downloads\usermod\models\decompiled 0.34\vn_dr_whooves_enh.qc(362): - could not load file 'vn_dr_whooves_enh_anims\ragdoll.smd'

The compiler does not find the file "vn_dr_whooves_enh_anims\ragdoll.smd" that should be here (based on info in the log):

"c:\users\owner\downloads\usermod\models\decompiled 0.34\vn_dr_whooves_enh_anims\ragdoll.smd"

The "c:\users\owner\downloads\usermod\models\decompiled 0.34\vn_dr_whooves_enh.qc(362)" part of the error message means the compiler tried loading the file given on line 362 of the QC file.

My guess is that you still have a folder called "vn_dr.whooves_enh_anims" (note the dot in the name). Change the folder name to "vn_dr_whooves_enh_anims" (underscore replaces the dot).

Post the full compile log because it shows what the compiler has already handled or tried to handle. In this case, likely the line before the error message shows what SMD file it tried to handle but had trouble with.

This line in the log says what's wrong:

Error opening c:\users\owner\downloads\usermod\models\decompiled 0.34\vn_dr.whooves_enh

The compiler can't open that file, which in this case means the QC file. Based on my own experience, my guess would be that the compiler does not like the dot in the name (the character after the "vn_dr").
SUGGESTION: Change "vn_dr.whooves_enh.qc" to "vn_dr_whooves_enh.qc".

The Models section on this page[sites.google.com] might help, particularly number 4 that talks about using $includemodel.

Import the reference and physics mesh SMD files into Blender. Rotate the physics mesh to line up with ref mesh (should only need a 90 or -90 degrees on one of the axes). Apply rotation. Export the physics mesh overwriting the existing one. Compile.

"Running through Crowbar" is an ambiguous statement. Crowbar has several different tasks it does. To understand what the cause is, it is far better to describe what you did more exactly.

For example:
1. Decompiled (via Crowbar) a model from Garry's Mod Workshop [link to addon].
2. Without changing anything, compiled (via Crowbar) the model for Garry's Mod.
3. Placed compiled model in Garry's Mod addons folder [or w/e you do for that game].
4. Saw weird mess of a mesh (as pictured).

Without knowing the exact steps, I would guess that the rigging (weightmapping) was messed up in Blender. If you made no changes to the decompiled files and then re-compiled as in my example steps, then that might indicate that Crowbar messed up. More likely though, the original model files are messed up.

I understand your request and I might implement some form of the option.

Technically, I will have Crowbar *not* rotate anything and have the user figure out when to rotate, because nowhere is it explained why some models are rotated differently than other models. There should be some way for Crowbar to tell which ones should be rotated because the games that use them show the models correctly no matter what rotation is used. I just have not figured out what signals it (and looks like Cannonfodder never did either).

Yes, it sounds reasonable that compiling the animations with separate QC and using $includemodel in the model's QC should get around the error.

Looking at the source code for studiomdl.exe (the model compiler), the compiler found over 1524 SMD and VTA files used by the QC file. I am not sure if other files are included in the total.

To avoid the error, it looks like you have to remove some of the SMD or VTA files from your QC file. There are ways to have different sequences share the same SMD; look them up on the VDC wiki.

This line means it completed compiling the model files:
Completed "wall_dest_256x128_01.qc"

The CDynamicFunction lines are useless to us as modders and should be ignored.