Initially the Lions chief thought the call to award a spot-kick – Steve Morison nudging Daniel Ayala inside the area – was harsh on his side.
Jordan Hugill converted his kick to cancel out Jed Wallace’s first-half opener.
“I saw the angle the Sky cameras had on Saturday evening and I can see why the ref has given the penalty,” said the Millwall manager. “Steve puts himself in a position he doesn’t need to be in. As soon as you raise your arm – albeit there is minimal contact – you give the referee a dilemma.
“But there were fouls on our players from set-pieces in the first half. Shaun Hutchinson was certainly rugby tackled to the floor at one stage.
“There is a frustration because we did more than enough to win the game.
“Lee [Gregory] should’ve scored from a knockdown in the first half, Jed is one-on-one with the keeper and Mahlon [Romeo] had a chance just before we conceded.
“It was up there as one of our best performances this season.”
Millwall went with a 4-3-3 formation at the Riverside with Ben Thompson, Shaun Williams and Ryan Leonard in central midfield – Jed Wallace and Ben Marshall supplying the width behind striker Lee Gregory.
“We’ve used the 4-3-3 at various times this year,” said Harris. “Mainly as a go-to situation in a game to get a foothold, to get back in a game or to see a game out.
“There are different ways to do it – with and without a targetman, or a targetman in a wider area. I felt for this game, presuming Boro would play five central midfielders as they did the weekend before, that it was important that we competed.
“Having the three in the middle of the park and the two wide players come in and play at times, I knew it was going to be important to try and overload that area and dominate the ball.
“It worked extremely well. We found different ways without playing aerial balls and diagonals at times. On the ground we found ways we could get in down the sides with forward runs – not just from Lee but Ben, Ryan and Shaun made forward runs as well.
“You saw the quality on the counter from Jed.
“It worked well for us and it’s certainly an option for us again in the future as a system. I’d have liked to have played it at various times against certain opposition this year but with Shaun being injured and Ben not being with us it wasn’t possible.”