I don't see any issues with the attached file. Also don't see smd_bone_vis object there. Is it that exact file you've been intending to share? :)

Ah, found the object now. It's in "Blend FIle" of outliner but not in "datablocks", which seems a bit strange for me. Also, what does it exactly means "freeing custom bone object"? Just removing it?

By "freeing custom bone object" I mean that the error occurs while freeing the scene if there are custom bones present. I missed out the all-important repro step #2 of opening a new file, sorry!

Edit: I can't edit the report, even though the error message says that the bug owner always can..?

Weird that it's not in Datablocks too, it's right there for me.

Cant redo the bug, tried running the script in bone_shape_crash.blend then removing the scene. No error printed.

Removing the scene won't repro, you need to unload the whole blend file.

It turns out that the appearance of console errors differs between builds, but the bug remains. Add a breakpoint at action.c:720 (the id_us_min call in BKE_pose_channel_free) and you'll see that pchan->custom has already been freed.

Ok, I can redo the bug now too,
Simple fix would be for pose-bones not to be object users.

(IIRC they weren't always object users)