This happened before 9-11, for what it's worth.

I was doing something like a mileage run - it was a fare that allowed so many coupons/flights for a flat rate, and I had arranged an extremely circuitous routing in order to maximize the miles from the number of flights available, including one pair of segments that essentially dropped from the upper midwest down to Texas and went back up again. Stopover in Houston was about one hour.

I got off the plane, wandered around for a little while near the gate, then sat and read waiting for the flight to be called. From time to time I noticed one guy looking at me, and when the flight was boarding, he and another man came over, showed airport security credentials, and asked if they could ask me some questions.

I had no objection to hearing questions (although I might, in the proper circumstances, object to answering them), and so when they asked about my unusual routing I explained. They in turn explained to me that when the "unusual" routing came to the attention of the "authorities" (I didn't ask how that came to happen), they felt it looked like a courier or smuggler run, and had observed me to see if there was a "brush-past" or "hand-off" to someone or if I got or left something at a "dead drop".

I guess it could look like smuggling or spying (industrial or otherwise) from the routing and short layover, and that in itself could be suspicious.