Sadly this is not uncommon. Have had it happen more than once myself. For example, once (well before covid-19, obviously) MU couldn't check me in (which is by itself odd, as MU in the US, at least here in HNL, print Delta logo boarding passes, use Delta terminals and Delta ground staff), as there was no record of me on the MU flight. DL check-in staff (working for MU) called DL and there were three levels of escalation to someone "in Atlanta" to finally reissue the ticket, something like six or seven people on the call to fix it. Thankfully I had went to the airport early - it took nearly an hour. Then on the plane there wasn't a meal catered for us (in J), so the J pax were given a choice of a 2+ hour delay while two more meals are catered, or to "eat light" and have the FAs make 8 meals for 8 J pax out of only 6 catered J meals. After some commotion, everyone settled for the latter. The MU crew did a good job of this and making 6 J meals feed 8 pax, while the pilots got an extra smoke break amidst the delay (even before the plane took off, which is usually when they light up in the cockpit).

Very important to always check with the operating carrier carefully that you are both on their PNR and that the correct ticket shows, and if at all possible do OLCI with the operating carrier at 24 hours out. (Not just DL but with all airline tickets.)