Well as I recall it was pretty uneventful "wet spaghetti" launch for both crafts. I'll try to "dry" dock crafts on Kerbin. I'll report the results. Is there any way to produce more detailed log? I'm willing to put more effort into it.
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Results of "dry" docking ... I used new save and I put together allot of cars docked, undocked and mess around with them the undockable port was not reproduced. I even built small craft powered by RCS and hack gravity and to the same result - not reproducible.
Trying now with smaller craft in orbit