The first and most crucial was the award of a penalty to the home side just a couple of minutes into the second half with Erik Edman adjudged to have handled inside the area.
That led to El Hadji Diouf opening the scoring from the spot.
Just five minutes later and we were denied a penalty when Bolton's defensive wall blocked Fredi Kanoute's free-kick.
The lads near to the incident were convinced it should have been a penalty and referee Mike Dean ended up booking both Fredi and Ledley King for their protests.
Jermain Defoe came off the bench to equalise after 68 minutes but 60 seconds later Fredi was sent off for a second bookable offence.
There were few chances after that until Bolton netted twice in the final minutes to secure a 3-1 win.
Coach Chris said afterwards: "You always know in coming to a place like this that it will be a difficult game, you will be up against a few aerial battles and there is going to be some pushing and shoving.
"I didn't see the first incident myself but I've spoken to numerous people who did and they all thought it was an incredibly harsh decision considering the type of game this was.
"The penalty shouldn't have been given and if any of our lads were aggrieved then rightly so.
"There's always going to be contact. We thought it was ball to hand and that Erik had certainly been impeded before that.
"Soon after we had our own claim for handball at the other end, but we ended up getting two bookings from that incident.
"These are two lads that rarely get booked, so that says how strong they felt.
"When Jermain scored we were happy to be back in the game because we're realistic enough to know that a draw here is a good result.
"We also knew we would have opportunities and we did that even with 10 men, we broke and if the final ball had been better we might have scored.
"But, of course, once we were down to 10 men we would have settled for a draw."
"We were more than annoyed that Fredi got his first booking and that obviously led to him being sent off."
Hughton, though, is convinced Spurs can again find the form that saw them win six successive matches before the start of the new year.
"If you look at our season the players have shown the character to come through bad periods," added Hughton.
"We've been fortunate enough to bring in enough players through this transfer window and we are looking to have a good run-in to the end of the season."
In total contrast, just as Tottenham have capitulated, Bolton are on the rise as this was their sixth successive victory after they ended 2004 with six straight defeats.
Delighted Bolton boss Sam Allardyce said: "Just as you get into the habit of losing, so you can get into a habit of winning.
"We feel that no matter what happens we are not going to lose at the moment and that's down to the hard work of the team and our determination not to concede a goal.
"That's the main reason why we are shooting up the league. As a team we have shifted our mentality from being attack minded to not conceding.
"Some of the bounce of the ball and rub of the green is now going in our favour and we are capitalising on it.
"That is why we are winning instead of losing.
"We've now done the double over Tottenham this season, and God knows when we last achieved that against a side that has spent a lot of money and with its fan base, history and reputation.
"It's no mean achievement what we have achieved tonight and this season."
Hughton, meanwhile, confirmed Spurs are to sign exciting Derby teenager Tom Huddlestone for £2.5million in the summer.
Hughton said: "He is a young, talented player who will mature and develop with the traditions of the club."
Chris Hughton felt key decisions went against us in Tuesday night's loss against Bolton.