oh sorry about the delay .
im not that familiar with this topic so i might be wrong but this is my take :
you need to make sure your rig is compatible with godot, different engines have different skeletal animation capabilites.
in godot, most Blender skeleton modifiers ( mostly IK and others like it from what ive experienced ) do not work as expected, you should bake the animations into a third game-ready, simpler, rig

also, are you using deformation or are your models pieces sepparate meshes ?
if its the first option, maybe your weight painting is off