Leighton Baines' double - the second from the penalty spot - put Everton 2-0 ahead at half-time and, although Shane Long pulled a goal back, the Toffees held on to leave the Baggies with only one point from a possible 15.
"If you go 2-0 down in the Premier League it is difficult to get a result," Clarke said.
"We had a go in the second half but the key moment was the penalty on half-time - if we'd come in 1-0 down we would have had more chance of getting something from the game.
"I don't think we were great but I don't think Everton were particularly great either, it was a nothing game.
"We were quite comfortable until we gave away a bad goal but even after that I thought we were in a decent place and the penalty on half-time made it much more difficult."
Clarke has an injury concern over midfielder George Thorne, who was carried off with a knee injury in the first half and will be assessed on Thursday to discover the extent of the damage.
"Fingers crossed, but it doesn't look good," Clarke added.