No. I’ve done many short haul flights like that without problems, including in the US. (For example Houston to Mobile, only to return the same day). Despite perpetually looking like I’m a confused foreigner (mostly because I am a confused foreigner), I’ve had no noteworthy issues with the TSA.
Only thing I can think of was that one time they did not understand that, yes, you can in fact have a TWIC and a C1/D visa without working for an airline. Cost me maybe 5 minutes extra.
Sometimes the duration of your stay is a short one, and your baggage (or lack thereof) will reflect that.
Primarily anuses (anii?), some of which still have feces on them.