Can someone smarter than me explain how exactly 401k fees are assessed? My wife's 401k has $3 taken out of it as a fee once a quarter; my 401k doesn't even have

Can someone smarter than me explain how exactly 401k fees are assessed? My wife's 401k has $3 taken out of it as a fee once a quarter; my 401k doesn't even have that. Or are the fees built into the returns? (e.g., my 401k is up 5% for the year, but without the fees it'd be up 6% or something like that?)