Could result in your not getting pre-check on your BP. This happened to me with a recent AmEx booking on AA (for a flight that was the next day). I booked it then checked in, didn't have pre-check even though AA has my KTN etc and have gotten pre-check on dozens of AA flights without issue. I called them up and while they changed my name in the PNR, there wasn't a way for them to re-send the BP through whatever system it goes through to get pre-check. They said I could try at the airport but I couldn't risk not getting it as I would be cutting it close for the flight as-is.

Bottom line, I was able to cancel the booking with AmEx and get the ticket re-issued. Per advice from the AAgent, I left the middle name field blank at the AmEx website this time. She advised that many OTAs add the middle name to the first name which is what was causing the pre-check issue. After re-ticketing with middle name field blank, I got pre-check no problem. I believe AA "filled it in" to match my KTN middle name since they have it on file in my AAdvantage profile.

tl;dr - leave middle name field blank when booking via OTA.