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Nikki Bull issued a public apology to Ebbsfleet United on Saturday night.
The Margate manager ran onto the pitch at Stonebridge Road to celebrate when Lewis Taylor scored in the 91st minute to earn Blues a dramatic 2-1 win.
He was confronted angrily by Fleet striker Danny Kedwell although the pair later made peace.
Bull said: "I’d like to apologise to everyone at Ebbsfleet for running on the pitch when we scored at the end. It’s not really acceptable for a manager to do that.
"Six weeks ago, I was a player. I wore my heart on my sleeve as a player and, unfortunately, I’m doing that as a manager. I got caught up in the moment but it’s not acceptable.
"I let myself and maybe my own club down, so apologies for that.
"If I was a player and I was in goal, I would have been down there celebrating with the players but I’ve crossed the line now so I’ve got to learn not to do that.
"I’ve come up against Keds many times. He’s someone that I don’t know away from the pitch but I respect him as a player and he’s got the same passion I have.
"He was telling me ‘get off the pitch, it’s not acceptable’ and it wasn’t.
"I apologised to him at the time, we shook hands at the end, we had a chat in the tunnel and all’s good."
Margate took an early lead through Kane Wills but Kedwell equalised in the first minute of the second half before Taylor struck for his fourth goal in two games.
Bull said: "I thought the players were excellent. We had a game plan and apart from the first five minutes of the second half, which seems to be our Achilles heel at the moment, we stuck to it.
"To go and get the winner at the end, we were piling men forward… I made the decision after 65 minutes that every sub I was going to make was going to be positive.
"Ebbsfleet changed it at half-time, they swapped (Danny) Haynes on the wing and we didn’t deal with that for the first 5-10 minutes of the second half. It was an excellent change from Daryl (McMahon).
"I looked at the bench with 30 to go and I thought ‘OK, let’s make it a game of football, it’s going to be end-to-end and we’re either going to win it or we’re going to lose it’ and fortunately we won it."