During the first half, Marriner disallowed a George Saville goal for a foul on Tim Ream, while in the second half, Millwall's Tim Cahill brought down Ryan Fredericks with an apparent elbow strike, which went unpunished.
When asked by News Shopper about the Cahill incident, Harris said: "I didn't see an elbow, I was on the other side of the pitch. The referee thought he had an excellent first half so presumably he thought he made the right decision on that as well.
"I thought there was a lot of protection for Fulham from the referee in the first-half. I thought he could have let a lot more go, but as he pointed out to me at half-time he thought he was 'excellent' in the first-half. Open quotes, he was 'excellent', closed quotes."
Millwall remain sixth in the table following the defeat at The Den.