The Stags played the young Toffees in the EFL Trophy and the League Two side were beaten by them 1-0 through a late Youssef Chermiti penalty.
The Premier League 2 side won their first EFL Trophy match in the process and Clough believes that the decision to award them the late penalty was wrong.
The Stags boss stressed that his side have not got decisions all season in similar situations in matches and insisted that they were on the end of an unfortunate decision which cost them the match.
Clough believes it is no surprise that managers are so unhappy with decisions being made by officials.
“Yes, soft is an understatement, not a penalty, end of story”, Clough told the Stags in-house media.
“Unfortunately, we are at the mercy of these decisions.
“And even in games like this they are result changing and result deciding decisions.
“I have watched in the last few weeks especially, but all-season Aiden Flint from corners, people not looking at the ball, holding him, wrestling him and everything and then that’s given for a penalty tonight!
“It’s no wonder that everybody is up in arms at the moment, it really isn’t.”
The young Toffees fielded a returning-from-injury Seamus Coleman for 66 minutes against the Stags while summer signing Chermiti played the whole match.