Coach Dieter Hecking told Sport 1 that referee Mark Clattenburg "will know he had his say in the outcome of the match" after Borussia Monchengladbach went out of the Europa League.
Hecking's side were beaten by Bundesliga rivals Schalke on away goals, having been 2-0 up at half-time in the second leg after a 1-1 draw at Schalke last week.
Schalke pulled one back shortly after half-time through Leon Goretzka before Clattenburg awarded a penalty to the visitors after the ball hit Gladbach midfielder Mo Dahoud on the shoulder.
Nabil Bentaleb scored to put Schalke through, and an angry Hecking said: "Mark Clattenburg waited a long time until he made the call.
"I am not sure what he was thinking -- that's surely not a handball. If the ref looks at the scene again, he will know that he has had his say in the outcome of the match."
Schalke sporting director Christian Heidel, also speaking to Sport 1, said: "I have to say that I'd be raging if I were on Gladbach's side.
"The ball hits the upper arm, sure -- but that's certainly unfortunate."