The 20-year-old defender was named in the starting eleven on Friday night but pulled out of the team after the warm up
Colwill watched on from the sidelines as the Blues played out a 0-0 draw at Stamford Bridge and will need a replay to progress into the last 16.
Asked about Colwill's fitness, Pochettino said: “We don’t believe it is so bad. It is a small issue and he felt uncomfortable. I hope he can train tomorrow or after tomorrow.”
The Blues boss was full of praise for academy star Alfie Gilchrist, who started against Premier League opposition for the first time since making his debut last month, adding: "[He was] really really, good.
"The most difficult thing is to manage the stress. He knew he wasn't going to play but then he was going to play.
"All the young ones need time to relax and not spend energy thinking before the game. Of course. It's really important for his career. He needs to compete with different players in his position.
"It's important for all the academy players who have the opportunity to play to cope and show they can play for Chelsea. We are so happy in the way he's producing."
Klopp's shock announcement that he will leave Liverpool overshadowed the cup matches on Friday night.
Pochettino paid tribute to the German manager, who will leave Anfield at the end of the season. “I was in shock," he added.
"Today, I was working and received the news. It is really sad. We already missed him. When I was sacked from Tottenham, the first message I received was from him.
"The job he has done with Liverpool is amazing. He wishes to rest and go away for a little bit. I think he deserves but it is sad for people who love football.
"He is a great character and Liverpool and English football will miss him. When he arrived, his first game was against us [Spurs] at White Hart Lane.
"We drew 0-0. His legacy is massive. I congratulate him and his coaching staff. He deserves the praise he will receive from now until the end of the season.”