Klopp's team encountered a similar problem last season and the German said he supported Mourinho, reiterating that more needed to be done to help sides in European competition.
However, the Portuguese tactician was slammed by United great Roy Keane, who questioned whether the club was too big for Mourinho.
"It is all about using the experience you have and when you think of experience I heard what Jose Mourinho said and what the pundits think about it," Klopp told UK newspapers.
"Last season we had the same experience. It was really hard.
"We played Villarreal and then Swansea at 12. If you want to help you should not do that. I know it is contracted, but 12 or 4pm? Don't play then.
"Don't make it more difficult than it should be. We thought the same. We thought it was really hard. That was an experience."
Klopp's men are fourth in the Premier League – six points ahead of United but having played two more games – and have a trip to Manchester City on Sunday.