The Royals boss felt his men performed well in the loss, but were made to pay for missing a host of chances in the league meeting.
Lee Wort's 15th goal of the season fired Portchester in front inside seven minutes but that would be as good as it got for the visitors.
A combination of some outstanding saves from Blackfield goalkeeper Tom Chambers, who was man of the match, and some poor finishing from the Royals meant they only managed to net one goal on the day.
Carter was also angered at the failure to not award his men a penalty in second-half stoppage-time.
Ronan Curtis' Portsmouth future spelt out by trusted source well in the know - with advice on where to play Irishman added, too
Former Portsmouth keeper Alex Bass suffers tough night on and off the pitch as he makes Sunderland debut following Fratton Park exit
Portsmouth boss Danny Cowley makes transfer admission as former Luton and Millwall midfielder edges closer to Fratton Park exit
Former Portsmouth, Ipswich and Bristol Rovers striker joins Port Vale - just eight months after moving to Fleetwood
Former Charlton and West Ham midfielder ready for next step at Portsmouth after standout showing against Cardiff
The Portchester boss said: ‘It was a frustrating afternoon. Their keeper probably had the game of his life yesterday - he got man of the match actually - which says all you need to know about the game.
‘He (Blackfield goalkeeper) was a big lad and he just managed to get his fingertips to everything.
‘Joe Briggs shot - the lad is literally on the line (goalline) - he only put his arm out slightly but it hit his arm before going in the net.
‘The referee said his arm was by his side, but it hit his arm. Sam Pearce then got sin-binned from that then Conor Bailey was dazed after taking one in the face so we were down to nine-men.’
Wort's early opener was cancelled out by Sami Makhloufi's leveller after 32 minutes.
Owen Fee then fired Blackfield in front a minute past the hour before the game's controversial moment.
Portchester were up in arms as they were not awarded a penalty after a home player appeared to handle on the line late on.
The Royals had Sam Pearce sin-binned following his protests at the spot-kick not being given while the visitors spent a period down to nine-men after Conor Bailey was briefly forced off after the ball struck him in the face.