Andy Awford admitted he was fuming after Mark Byrne’s controversial goal was allowed to send Pompey to defeat.
The Newport County midfielder’s 67th minute shot from distance crept in at the far post.
Yet with Aaron O’Connor in an offside position and in Paul Jones’ line of vision, the linesman raised his flag – only for the goal to stand regardless following a discussion with referee Michael Bull.
The Chelmsford referee also turned down two strong penalty shouts, both of which Awford felt should have been awarded.
And Pompey were denied what would have been at worthy point at Rodney Parade.
He said: ‘The referee has explained the decision to me - which I don’t agree with.
‘I have to be careful, if you say too much you end up getting yourself in trouble.
‘The criticism I have of us today is we should have scored, we had a lot of the ball in their box to score.
‘But when you lose the game through something out of your hands, it is clearly offside in my opinion and hasn’t been given. That is the disappointing thing for me.
‘We also should have had two penalties and neither were given.
‘We’ve had 17 shots and they have had eight, which shows you where the ball was for the majority of the time.’