One speculation I could add is that, when the probe hit the cone, which always causes a change in attitude since the probe rarely hits the cone exactly head-on, perhaps the Progress tried to correct for this attitude change without being aware that contact had already been achieved? Or something along those lines?
Undocking is planned at 3:48 UTC on Sunday/11:48 pm EDT on Saturday night
Will future Progress-MS flights be grounded for a while due to the unexpected thruster firings that Progress MS-01 went through?