Gareth Southgate feels disappointed with the referring decisions which he felt were major factors in the defeat at Fratton Park.
Middlesbrough went 1-0 up in the 24th minute thanks to a Mido finish, but crumbled in the second half as a Jermain Defoe brace killed off the visitors.
But the Boro boss was aggrieved with a couple of decisions which on another day he feels could have swung in their favour.
As Portsmouth broke in the 59th minute which led to Defoe's equaliser, Boro had Mido injured on the floor and also new signing Didier Digard waiting to come back onto the field.
When Sky Sports asked whether he thought play should have been stopped, he said: "Yes I do.
"We can't blame referees for results but the other thing was we had Didier Digard off the field at that point waiting to come back on.
"The ball went up the field and back down the other end and he was still stood on the side so we were down to nine when the goal went in so I don't think it was helpful anyway."
But despite the loss, Southgate conceded that Pompey were by far the better team in the second half.
"We played really well first half and we didn't do enough going forward as a team, we didn't keep the ball well enough and pose them problems in the second half.
"If you invite as much pressure as we did then you do run the risk of conceding the type of goals that we did," the Boro manager said.
More decisions against the Teessiders came in the final quarter as Stewart Downing was brought down in the box but referee Stuart Attwell waved play on.
Portsmouth countered and Defoe gambled on a loose clearance to secure the three points for Pompey.
Asked if it was a penalty Southgate said: "It's difficult to say, I'm bound to say yes.
"I think if it was anywhere else on the field you might've got a free-kick but I haven't seen it again. We can't sit and harp on about referees."
Despite the disappointing trip, the former England defender was pleased with his players' work-rate.
"The players are giving absolutely everything which is what you want, we just stopped doing things that got us into the lead and we've got to learn those lessons really," he added.