Ole Gunnar Solskjaer's side will play three matches in five days after their clash against Liverpool on May 2 was postponed due to United supporters protesting inside and outside of Old Trafford against the Glazer ownership.
Solskjaer was furious with the amended fixtures and fielded a weakened team in the 2-1 defeat to Leicester City on Tuesday ahead of the rearranged match against Liverpool on Thursday.
When asked if Solskjaer's decision to make a host of changes was frustrating, Klopp told a news conference: "It was the lineup that I expected because I knew he had to make changes.
"They play on Sunday, Tuesday and Thursday and I've said this many times, with all the things that happened, to play Sunday-Tuesday-Thursday is a crime. It's not the fault of Ole Gunnar Solskjaer and the players, so if it was me, would I have done the same? Yes.
"We are late in the season, United make it through to the European final and now you get Sunday-Tuesday-Thursday, that's not possible. I'm not the guy who makes the fixture list but when we thought about how it could work out on the day the game got cancelled, we made out fixtures on the bus and there was no Tuesday-Thursday games.
"But that didn't happen and the explanation from the Premier League was that no other teams should suffer because of what happened in Manchester but that didn't work out pretty well.
"But, if we don't qualify for the Champions League, it is not the fault of Ole Gunnar Solskjaer's team selection or the Premier League -- it is our fault."
City were confirmed as champions after United's defeat and Klopp hailed Guardiola as the best manager in the world.
"I texted Pep last night and I have already texted Ilkay," Klopp added."Very well done after a very difficult year for everyone, not just in football.
"What they have achieved so far is exceptional. When you bring together financial resources and football knowledge, you have a good chance to create something special.
"This is obviously the case. They have a brilliant squad and the best manager in the world. It is always a joy to play against them because it's such a massive challenge.
"You can beat them but you have to be at your very top. Well deserved and congratulations."