Opposition view: Embleton 'mind-blown' by referee decisions but backs controversial penalty call
The game had been light on controversy up until the 84th minute when Orient, trailing 1-0 at the time, were awarded a penalty for handball against Wharton.
There was no doubt the ball struck Wharton's arm but he looked to have been blatantly pushed by Jordan Maguire-Drew as the cross came into the box, which left Town's players incredulous when Young pointed to the spot.
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Hide AdJosh Wright converted from 12 yards but the drama didn't stop there as all hell broke loose with Wharton dragging Orient substitute James Dayton to the floor in an attempt to get the ball before nearly all 22 players got involved.
Both Wharton and Dayton were shown straight red cards and then the home side almost won it during the eight minutes of added-time as Cobblers just about clung on.
"I don't think James expected to be red carded," said Embleton. "There was some mind-blowing things that happened during those moments.
"First thing's first, the ball's gone in the box and we've won a penalty for handball and it should be a yellow card because the guy's punched it away from Jordan Maguire-Drew's head.
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Hide Ad"The fourth official told me it's not a yellow card because he's in the air but I don't know how that has anything to do with it.
"That was ridiculous and then the ref spoke to me at full-time and his reason was that there was 'too much going on' but that's a cop-out because it all happened after the penalty was taken.
"He should be given a yellow card and my mind's blown. Then James Dayton gets sent off and yet (Vadaine) Oliver, who had been taken off by Northampton, ran half the length of the pitch to get involved but no-one saw it.
"But they saw James Dayton do something that I didn't manage to see so there's a lot there that doesn't make a great seal of sense."
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Hide AdOrient were comfortably outplayed before half-time as Ryan Watson lashed the Cobblers into a 43rd minute lead, but theywere much-improved after the break.
"It was mind-blowing the difference between the first-half and second-half," Embleton added. "It was astonishing.
"We looked edgy and we looked nervous, which is to be expected, and I felt our performance really reflected that for everybody because we're all a bit nervous at the moment.
"I do wonder to a degree whether their goal settled us down at half-time because our boys came out with a nothing-to-lose attitude and had a right go.
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Hide Ad"It's happened on a few occasions this season where we've had a poor start and a grandstand finish. There's never a dull moment here but the way we applied ourselves in the second-half was to be applauded."