Hull have been fined £145,000 by Uefa for breaking Financial Fair Play rules, while Liverpool were cleared.
City boss Steve Bruce feels the penalty was a result of the costs incurred getting Hull out of the Championship.
They must pay an additional £290,000 if they are not compliant next season.
"It's tough on us because the only reason we've come under investigation is a) we've qualified for a Uefa tournament and b) because of when we were in the Championship," Bruce said.
Hull exited the Europa League at the final qualifying round stage.