He will be even more sorry Arsenal didn't take their chances at the Amex Stadium on Wednesday night. Having taken an early lead through Pierre-Emerick Aubameyang, Arsenal should have coasted to three points.
They certainly had the opportunities to do so. But by the end, it was Brighton who were in the ascendancy following Jurgen Locadia's equaliser. And Emery's frustrations were laid bare in the closing stages as he took his anger out on a nearby water bottle - only for it to, albeit slightly, strike a spectator.
There was no malice in the Spaniard's actions. Maybe if his side had shown greater intent, they would have left with three points.
Credit to Arsenal for quickly identifying the fan and handing him Laurent Koscielny's shirt as a gesture of good will. It is Christmas after all.
But when Emery analyses this performance he'll conclude his team were far too generous.
'I think this draw is not the best, but not the worst,' said Emery. 'It's a difficult moment for us because we have some injuries.' Not the best way to gear up for league leaders Liverpool on Saturday.But truth be told, Arsenal should have been home and hosed by half-time.
Even before Aubameyang handed them a seventh minute lead, Arsenal would have been ahead had it not been for Mat Ryan's excellence in the home goal to deny the Gabon striker's clever looping effort.
The opener, when it arrived was clinical - Aubameyang smashing past Ryan with a curling shot following tenacious build-up play from Alexandre Lacazette.
This was the Spaniard's first taste of football over the festive period; Aubameyang's goal made working at Christmas far easier to bare.
Arsenal were purring, Brighton's players looked like they'd indulged in one too many Turkey sandwiches the night before.
But Hughton's side, as they so often do, hung in there. Clung on for dear life. 'That 15 to 20 minute period was probably the most important of the game for us,' admitted Hughton.
'If they score the second then it's hard to score two or three against that level of opposition. We had to hang in there.' Brighton were clutching at straws in the 25th minute when they claimed an equaliser, even though Glenn Murray had clearly kicked the ball out of Bernd Leno's hands.
But slowly, they were showing signs of life. Five minutes later, Leno saved from Murray after Solly March's pass. One minute later, however, Arsenal should have doubled their advantage.
It looked for all the world Aubameyang would double his tally; he didn't bank on Ryan producing a brilliant instinctive save. The stop proved pivotal as Brighton levelled just five minutes later.
Davy Propper's raking pass was more hopeful than accurate - but somehow Stephan Lichtsteiner made an utter calamity of dealing with it. The former Juventus star should have simply nodded away, instead he got himself caught under the ball.
Locadia gobbled up the opportunity, rounding Leno before stroking into an empty net.
The Amex erupted. You'd imagine there'd have been a similar reaction from Emery at half-time.
Having taken this game by the scruff of the neck, Arsenal were punished for taking their foot off the gas. Emery responded by hauling off Mesut Ozil at half-time, replacing the German with Alex Iwobi.
Ozil was brilliant on against Burnley on Saturday. Four days later he suffered the ignominy of being hooked at the break.
'It was a tactical decision, I wanted to control possession better on the pitch,' Emery explained.
No matter how Emery dresses it up, yet more doubt has been cast over the Arsenal No 10's future at the club. With every passing week, it's plain to see Emery simply does not trust Ozil on tough away days.
Not that the substitution sparked the Gunners into action; if anything Arsenal were poorer without Ozil as Brighton roared into the second half.March's long ranger was turned round the post by Leno in the 50th minute before Propper snatched at an excellent chance after being set-up by Locadia.
Emery made another change in the 62nd minute - introducing Aaron Ramsey for Lacazette, who looked far from happy from being hooked again.
But Emery needed to intervene, his side a shadow of the team that started this encounter.
In the 76th minute, March fluffed his lines in front of goal before Locadia flashed a shot narrowly wide as Brighton pushed for a late winner. By now Arsenal were ragged in defence and laboured in attack. Like Brighton in the first half, they were hanging on.
'If anyone was going to score a second, then it looked like it would be us,' said Hughton.
Yet the Gunners nearly scored a flukey winner in the 84th minute when March's attempted clearance ricocheted off Iwobi and narrowly past Ryan's post.