A pair of goals from Luis Suarez and a late strike from Paulinho were enough to grind out an 11th win from 12 games and stretch their lead at the LaLiga summit to seven points.
"Maybe 3-0 is a bit excessive; they have contributed so the distance shouldn't be that wide," he said in his post-match news conference.
"We have had a high rate of success, but this is football. I recognise the effort Leganes has made today despite the defeat.
"We all like to win and have many chances and the opponent does not make any, but it is not always the case, they have been very combative. They made it difficult to play inside, it was a complicated game, and I do not deny it.
"I think the result is good, we have not been brilliant and we know we have to improve, but I repeat, we value the rival a lot."
Goalkeeper Marc-Andre ter Stegen made a string of saves to preserve the comfortable nature of the scoreline, and Valverde was quick to praise the German.
"Marc-Andre ter Stegen is having a great season, he gives us a lot of confidence, we appreciate his saves," he added.