This is not Godot’s fault as far as I know, but the consequence of networking.
I will presume you are updating only the position and not velocity? I assume the authority is updating position with a velocity at 60fps and the peer is only getting snapshots at maybe 60fps or less, and no velocity. The network could add jitter and packets could come out of order. Unless you are using reliable which is never a good idea for fast game state updating.
Checkout my physics based syncher with a ring buffer.