The Magpies midfielder saw red for his stamp on his Spurs and England counterpart, which happened in front of the referee, 48 minutes into Sunday's Premier League game at St James' Park.
Earlier on in the game, Kane earned himself a booking for a foul on Lejeune, who had to be subbed off not long after, and the Newcastle manager claims there was a discrepancy in the outcome of the two incidents.
Benitez told Sky Sports News: "It was difficult from the beginning. We had to adapt things [after injuries]. The red card changed everything. I think we were defending well. We have to improve. We had our chances but we missed them.
"The Harry Kane tackle was worse than this one. It's more dangerous. We lost one player from that. We made a mistake, but I think maybe someone has to analyse these things to see what's more dangerous."
Shelvey has been sent off twice under Benitez at Newcastle, more than any other player.