People who perpetuate this type of conspiracy theory crap also don't understand that if the passenger is not able to check in on line it leads to more expense for the airline with having to have an agent check them in, right down to having to use one more piece of paper (vs having the passenger use their own.) and just having someone in the IT department set such a thing up.
It's a computer system. It will go down periodically weather for maintenance or glitches.
The other thing to consider is that if your name is close enough to someone on a watch list, per the TSA you cannot check in on line, but the airline is not allowed (per the TSA) to tell you this is why.
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