The Blues found themselves trailing by two goals after 28 minutes as the League One strugglers shocked the visitors.
By that stage there had been two stoppages of play after Reading fans threw tennis balls onto the pitch and into Pompey half as a protest against owner Dai Yongge.
Following the second occasion it happened on 16 minutes, an announcement was made that referee Martin Coy would abandon the match if it continued.
Mousinho criticised Pompey’s ‘Jekyll & Hyde’ performance in that first half as they fought back to win 3-2.
Yet while the tennis ball situation impacted on the flow of the match – he didn’t believe that was the reason behind their poor early display.
He told The News: ‘It impacted the flow of the game, but Reading had to deal with the same things. They didn’t have that sloppiness in the game, which we showed for the opening 30 minutes. They got on with it and didn’t seem affected by it.
‘I don’t want to blame the situation because it’s one we have to deal with if you want to be a professional footballer.
‘I was really disappointed with the way we played for 25-30 minutes, but even at 2-0 down, I thought we were going to get back into the game and we proved to ourselves that 15 minutes worth of good football could do just that.
‘It was Jekyll & Hyde in the first half. For the opening 30 minutes we were an unrecognisable team, then for 15 minutes once we took the kick in the face we were excellent.
‘We were fully deserving to get back into the game and – for half-an-hour after half-time – it then looked like only one team was going to get the goal.
‘We haven’t been as exposed and haven’t made that many errors and been as sloppy as that for a while. So to put that all together and concede the first and the second in the manner we did, we’ll have to strip back and have a look at what actually went wrong.
‘Ultimately, individuals and us as a collective didn’t perform well enough, we made poor decisions, didn’t track runners and weren’t aggressive enough. When we did get the ball we were far too willing to give it away.
‘And all of those things combined for Reading to be fully deserving of their lead – but we came back to win the game and I have to credit the players for that also.’
Tino Anjorin, Colby Bishop and Terry Devlin completed a remarkable fightback for the Blues.
It leaves them six points clear at the top of League One following second-placed Oxford United’s latest draw.