Spurs won via a double from corner kicks scored by Micky van de Ven and Pape Matar Sarr's late strike.
Asked if the scoreline was unfair, Moyes said: "I agree with what you say. I don't think that we deserved to lose 3-0 but if you don't defend set pieces well enough, then you're always liable to lose the game.
"It's not something that's been a big problem with us but it was today, whether that was because of the quality Spurs had or whether it was down to how poor we were defending it, then that could be argued."
Satisfied with Everton's performance, Moyes said his message to the players in the home dressing room was: "Some good things and, obviously, I'm annoyed because we don't defend our set pieces as poorly as that normally, so we'll need to try to improve on it.
"We've been pretty good at it. Overall, the play was good enough to earn more than we did today, we've just got to try to tighten up and finish off some of the good play and the chances we have.