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Herne Bay joint-boss John Embery felt his team should have had two penalties at Margate on Saturday.
Bay were the better team in the first half at Hartsdown Park but referee Jacob Miles opted to give them a free-kick on the stroke of half-time rather than a spot-kick.
The visitors were then on the end of a similiar decision late on in their FA Cup third qualifying round defeat.
"I thought it was a stonewall penalty in the first half, he gave it outside which I thought was strange but there you go," said Embery.
"It was in the box and I thought the one in the second half was even more blatant - it was a yard or two in the box. He has given free-kicks right on the edge of the box, even their manager was shaking his head.
"Referees have got to make a decision on the spot, maybe sometimes with a big crowd of 1,000 people that goes against you."
Embery was delighted with the performance of his young guns - but agreed that they needed to test Margate keeper Lenny Pidgeley more.
"The first half we had plenty of chances but we didn't pull the trigger enough," he added.
"We worked the ball into good areas and should have got something out of it.
"We had more possession, more chances and I think we surprised them. We could have took our chances and get a few more shots (away).
"That was the biggest problem. We had a great opportunity to get shots away but we over-played it or we took one touch too many. But it's because they are young and they will learn."
The Bay boss was not happy with the manner of the goals his team conceded - and with a bit of luck on their side they could have forced a replay.
"We shot ourselves in the foot with two mistakes for their goals but that's football," he said.
"On the first goal, we gave away a poor corner but we've got to defend better. It was a high cross, it had snow on it, and we have to put our heads on it and head it away.
"The second goal, Nassim Dukali has had a good game but he got caught a little bit and it killed us.
"It was a sickener for us, knowing we could have got something out of the game. It's a great achievement for us to get this far but we thought we could have gone even further."