Wayne Rooney struck both goals for the visitors in the 2-0 win.
"We're obviously disappointed, because the side that Manchester United put out was a team that we could have made the most of on Saturday," centre-back Tomkins told West Ham TV.
"Unfortunately, their qualities have obviously shown again with the two goals.
"The second one's unfortunate and the first is a great goal. We look at it ourselves as being a disappointing day."