The Ecuador international first picked up the injury in the 1-0 defeat at Manchester City and has subsequently missed the Latics' last two games.
But after coming through three training sessions in the week manager Steve Bruce opted to start the 23-year-old against the Cottagers.
The decision backfired as Valencia broke down after just 19 minutes of the 0-0 draw at the JJB Stadium and the former Birmingham boss admits he made a mistake.
"We have probably set him back two or three weeks," he told the Wigan Observer.
"Antonio trained during the week and thought he was fit, but hamstrings are injuries you really have to be careful with.
"You probably can't get away with only two or three training sessions when you're playing at this level."
It was a match to forgetten for Bruce after midfielder Michael Brown and striker Mido both had to be withdrawn before half-time.
MistakeBoth players had been absent from training during the week with Brown struggling with illness and Mido suffering a groin strain.
The Latics boss decided to gamble on the pair's fitness but again had to hold his hands up and admit that it had been the wrong decision.
"I messed up. I played too many players who weren't match fit or were only half-fit," he added.
"Mido was only half-fit, Brown had been sick before the game and wasn't right, and Valencia had only two or three training sessions.
"I put Hugo Rodallega in from the start and then Ben Watson came on after only 19 minutes, yet both hadn't started for six or seven weeks.
"With hindsight I wouldn't have picked the team I did. The one thing you can't do in the Premier League is play lads who are below their best.
"It doesn't do them or the team any good. Thankfully the back four were terrific and got us a point out of the game, we got away with it to that extent.
"But it was a bad day at the office. We didn't play well at all. In the two games against Fulham this season, they've given us more problems than any side have done.
"I thought they were excellent, so in many ways I'm pleased we got a draw and we're a point nearer to where we want to be."
The triple injury blow to the club is softened by the fact that the team have a rare weekend off next week after their early exit from the FA Cup.