Raith defender Simon Mensing, who had earlier appeared to bundle over Kris Commons, was penalised for a trip on the same player in virtually the same place.
Commons netted the spot-kick much to Mensing's fury to set Celtic up for a comfortable Scottish Cup win with James Forrest and Charlie Mulgrew adding the other goals.
While Lennon was unsure on the award given to Celtic he did feel his team had a stronger appeal denied when Raith defender Eddie Malone seemed to handle in the box.
Lennon said: "I didn't get a great view of it and I might agree with Simon. I haven't seen it again but it looked soft, but the referee was right there.
"But we could have had a penalty for handball in the first half, I have seen penalties given for a lot less.
"But the way Kris took the penalty pleased me, the game opened up and I thought we looked great in the last 20 minutes."
Mensing said: "I thought the ref got that one wrong - he went down too easily and I know that for a fact. I'm really disappointed with it.
"There was minimal contact but Commons is clever. The ref just said he felt it was a definite penalty. I would argue until I'm blue in the face that it wasn't but it's not going to change anything."