I might have figured out what went wrong with the ticket (just by trying to submit a flight feedback) - when I rebooked the flight the OTA made a mistake and booked us on the 6:00 morning flight instead of the requested 11.00 departure. So they most probably made a mistake by reissuing the ticket after correcting the outbound flight.
In the feedback form I could select the 6:00 morning flight as well as the 11:00 morning flight - so the incorrect 6:00 morning flight reservation wasn't removed correctly I guess. That causes trouble. Had a similar issue with a rebooked TK flight where we could not check in online - same error - according to their internal data we were still booked on two seperate flights for the first segment. Only the airport agents could solve the issue.