When crossing back to the U.S. side by foot is your name logged anywhere or do they just check your passport and wave you through?

I'm in the military and I'm worried about being caught in TJ.

They run your ID through a scanner.  They will know when you crossed and how many times etc.

There is a record keep by the computer of all ID used to cross the border.  I think it's purged after 90 days do to limited disk space.