Mulgrew, who won the prize last season, told reporters: "I still don't see how one Celtic player didn't have enough votes to get into the top four.
"It has been noted what we have been done in the Champions League and being so clear in the league so it's disappointing. It's baffling to be honest.
"It is definitely not paranoia. I've said how I feel about why at least one of our players should be involved in the top four. The nominations are not tainted at all. They have done very well, four good players who scored a lot of good goals and deserve to be nominated."
Mulgrew's comments come after Celtic boss Neil Lennon described the nominations as abysmal.