That is indeed odd. It sounds like it may have been a one-time glitch as I've been able to checkin for multi-segment itineraries even when one didn't have a seat assignment. It usually happens when there's a regional aircraft and all of the pre-assignable seats have been taken and one can only get a seat assignment at the airport.
What is/was the departure and arrival city of the first segment of your itinerary? Are you flying tomorrow or did this happen sometime in the past? I have a theory about what might have happened but until I know more details I can't be too sure.
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