• I can confirm the problem on 3.0
• No problem occurs on 2.93 with addon code from 3.0

So, the problem probably come from an regression or change of bpy python API

Run this code in 2.93 and in 3.0 get different result:

import bpy

mesh = bpy.data.meshes.new(name="meshnew")
obj = bpy.data.objects.new("test1", mesh)

obj.vertex_groups.new(name="vg1")
obj.vertex_groups.new(name="vg2")

bpy.data.objects.remove(obj)
obj2 = bpy.data.objects.new("test2", mesh)
print(len(obj2.vertex_groups))

Adding Python API tag, as it not seems to be relative to a specific addon

CC @Hans Goudey (HooglyBoogly) : is this expected (sorry, no time to check further today)?

Probably because of https://developer.blender.org/D11689 which moved vertex group data from the Object to the Mesh?

Can easily be fixed by moving the code that sets the name from object creation time (here) to mesh creation time (here).

There is never a situation where the glTF importer would have shared the same Mesh between Objects with different vertex group names to worry about btw.

What @Julien DUROURE (julien) observes is expected. The vertex group names are now stored on the mesh rather than the object.

What @Scurest (scurest) says sounds correct to me, I'm not sure exactly how the glTF importer works, but if it relies on the fact that the vertex group names will stay when replacing an object's data, it will have to change.

Thanks @Hans Goudey (HooglyBoogly) for your feedback.
I already prepared a patch to change glTF importer that I will merge soon.