Sorry to hear about the issues. Have you tried taking it back to the dealer to check?
If I recall correctly, my MY16 GTI would do the same from 1st to 2nd very early on... Drove me insane! After trying various things, I managed to replicate the issue. Basically, if auto stop-start was activated + the engine turns off while you're at a stand still, on restarting the shift would be harsh - guaranteed. The solution was to make sure stop-start was deactivated when in manual mode. Never had that problem since.
Not sure if it's the same issue you guys are experiencing but I thoughts it's worth sharing
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