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Television replays suggested a late disallowed goal from Maidstone substitute Alex Akrofi should have stood.
United looked to have forced a first-round replay when Akrofi met a flick from Tom Mills’ cross in the last minute of normal time but the linesman’s flag was up for offside and nine-man Yeovil held on for a 1-0 victory at the Gallagher Stadium.
However, it appeared the ball reached Akrofi via a Yeovil defender, rather than Maidstone’s Frannie Collin, meaning the goal ought to have counted.
Stones boss Jay Saunders said: “The first thing Frannie said was it came off the defender first. I suppose from the linesman’s view he’s not seen it that way.
“When you look at it, it’s very, very tight on the replay.
“But Frannie misses the header and it comes off the centre-back so in theory it’s a goal but sometimes they’re given and sometimes they’re not.”
Yeovil had defender Jakub Sokolik sent off for an ugly studs-up challenge on James Rogers after only seven minutes.
And having taken the lead through Wes Fogden early in the second half, they were soon down to nine men when keeper Artur Krysiak saw red for taking out Alex Osborn.
But the League 2 strugglers defended brilliantly against a Stones side who also went close when Jamie Coyle’s header hit the post.
Saunders said: “It made it difficult them going to nine men. They drop that bit deeper and it means there’s not a lot of gaps and it makes it harder for you sometimes.
“All in all, I’m proud of the boys. They had a good go, we caused them a lot of problems and on another day you win the game. Unfortunately it wasn’t to be.
“I honestly believe if we’d scored one we’d have won it maybe comfortably. We looked better when they had 11 men on the pitch. It’s just one of those days.”
Saunders saw defeat by nine men as a missed opportunity but reminded everyone of the task his National League South side were facing.
He said: “I think people got a little bit ahead of themselves labelling us the favourites.
“It’s a missed opportunity because they were down to nine men and we had a lot of the ball but we have to put it in perspective.
“We were playing a full-time team, a team that were Championship two years ago, a league side, full of league players.
“We were never favourites today but we gave a good account of ourselves.
“I think we looked good and we caused them lots of problems.
“I’d have loved to carry on the run for the club, the supporters, the chairman and the players but that’s part of the cup. Sometimes it goes your way and other times it doesn’t.”