An injury-time strike from Angel Correa saw Atletico win 1-0 at San Mames.
"These things can happen in football. It was a pretty tight game," Valverde said after the match.
"In the first half, they sat deep, trying to catch us on the counter-attack and we didn't manage to create chances from shots or crosses.
"In the second half, the game was broken, we had a goal disallowed, although it is also true that they escaped our press and attacked with more precision than in the first half.
"The match was 0-0, but at any given moment, the game could have gone one way or the other. We didn't take our chances and, in the end, they scored the goal.
"It's a bitter blow for us. If we couldn't win this game, at least we had to draw.It's a bitter blow for us. If we couldn't win this game, at least we had to draw.
"We are a team that fights, that tries to move forward, but sometimes we make mistakes and we make mistakes that we don't want to make. This is football."
The coach also said: "Every match is different. The first one was very tight. The second, against FC Barcelona, we tried to do the best we could. And in the last two, the other day we played very well and in this one, we had some good moments.
"At times we struggled to get into the rhythm we're used to in order to win. We're a good team, we know we're going to get better. It was a shame, but we have to keep going."