Connecting flights that don't meet the minimum connection time of the airport/airline.
So it might come up with a routing of a stopover of 45 minutes on skyscanner because those flights are available, but the airport has a minimum connection time of 60 minutes. So if you booked the "illegal connection" (which booking through the airline directly or a travel agent shouldn't allow you to do) and your first flight was delayed and you missed the second flight then the airline wouldn't be required to put you on the next flight for free.
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