There were a lot of people on this flight who were connecting on to other cities. We landed just barely in time to catch the last flight of the day to many of those cities, but most people had to be rebooked since that wasn't their original flight.
So we get off the plane and about two hundred of us need to be rebooked, and we get to the counter to discover a grand total of three people working there. To process two hundred people. Who all needed fast service. For a problem that anyone could have seen coming literally a day in advance.
A lot of people unnecessarily spent their nights in hotels rather than with their families that night, because nobody looked at what was going on and said, we should bring in some more people for this.
But yes, I'm sure it's all about bad incentives. Whoever takes the hit for overtime staffing doesn't also take a hit for hotel vouchers, even though it probably would have been cheaper overall for the airline to staff up and get people on their flights. (Not to mention the benefit of pleasing your customers.)
Follow the money, and all becomes clear.
Presumably the TSA managers will be rated based on their wait times, and therefore accountable when they're too lazy to staff the right number of people.
Last week I almost missed my flight at Oakland because they had everyone funneled through a single scanner. Two scanners were idle because they were "short staffed". That's not an accident or bad luck. That just means the manager was too lazy to do their job correctly.