The Belgian was back amongst the goals against Howe's Bournemouth, but the Cherries boss said Lukaku was lucky to still be on the pitch when the full-time whistle blew.
The incidents in question were when the 24-year-old striker did not receive a second yellow for a challenge on Harry Arter, after he avoided a caution for a late tackle on Nathan Ake earlier in the first half.
When asked whether he thought Lukaku should have been sent off, Howe said: "I did. I was having chats with the fourth official and I thought the first tackle was a yellow card in my opinion.
"I thought he was very late on Nathan [Ake]. We made that point to the fourth official and then of course he picks up another one which is a clear yellow - he should have been off the pitch."
Howe also had a few strong words for referee Graham Scott, who ran the game at Old Trafford.
"The referee missed a couple, I don't want to go on about referees again but you have started me off. He missed a couple of tackles from them and then the first tackle we make we get a yellow, that was difficult," Howe added.
"I just had a quick chat with him [the official] at the end."