Benjamin Sesko struck on 71 minutes to earn the points for United.
Branthwaite stated afterwards, "I think second half we dominated most of the half. We had some balls into the box and created chances. I think it's something as a team we need to get better at - putting those chances away.
"One lapse of concentration on the counter-attack and they've scored the winning goal. We've came in at full-time disappointed because we deserved more from the game."
On Everton's performance, he also said: "You can see the way we started the second half, we came out with a lot of momentum. There was a 15-minute spell in the first half where maybe they dominated possession but overall it's been a good game from us. As I say, a lapse of concentration and we get punished.
"You can't do it in the Premier League. We've been punished. They had one (chance) in the first half where (Bryan) Mbeumo went through the middle and if it's a better pass, he's probably through again.
"That was on a counter-attack, so we were aware of it at half-time. It's disappointing to come in and not pick up any points."