On Thursday the 28-year-old Brazil-born Spain international was granted his wish after months of acrimony, claim, and counter claim when Chelsea and Atletico agreed a fee reported to be in the region of £58million.
Costa joined the Blues from Atletico in July 2014, scoring 59 goals in 120 appearances.
The Blues’ last league outing saw David Luiz become the fourth man sent off for them this season, including the Community Shield.
And Hughes said: “I think they’ve had more sent off than in the whole of last year.
“So is that an anomaly or something prevalent throughout their squad, a discipline issue?
“I think last year they were quite good at taking things up to a line and not crossing it, and maybe they have just got that balance a little bit wrong.
“I think if you look at Costa, he was brilliant at it in terms of really taking it up to the edge, then stepping back, but affecting opposition teams.
“Maybe they haven’t quite got that ability in terms of (getting) the dark arts right on spec at the moment. But I don’t see them as a team with a discipline problem.”
Hughes admits he was a fan of Costa, who is set to leave Chelsea after months of acrimony to rejoin Atletico Madrid.
“It’s a shame, a loss to the Premier League,” Hughes said.
“I used to really enjoy watching him play and how he went about his business, because he was different - he had an edge to him and the reaction of other players to him was really interesting.
“He’s a top player and the Premier League should have the top players playing in it.”
Antonio Conte was reluctant to discuss the departing Costa yesterday, but suggested Alvaro Morata would benefit from being more like his predecessor as Chelsea’s leading striker.
Asked about his replacement Morata, who has scored three goals since joining from Real Madrid in the summer, Conte was more talkative.
Conte reckons “very polite” Morata can be more aggressive on the field, an aspect of the game Costa relished.
“I like him (Morata) because he’s a complete player and also he has a lot of room to improve in every situation,” Conte said.
“When I speak about a lot of room for improvement it also means this aspect, to be more (aggressive).”
Conte described Morata as the type of person a father would welcome with open arms if the 24-year-old were to come home with their daughter.
A smiling Conte stressed he was not talking about his own daughter Vittoria, who is not yet a teenager.
“If you have a daughter you hope for this type of person (to be) with your daughter, to marry your daughter,” said Conte, who also praised Morata’s goalscoring instinct.
“He’s a good finisher, he feels the goal in every moment.”
Costa’s public reputation as arch-antagonist contrasts with his private one and he was popular behind the scenes at Chelsea.
Despite Costa’s Chelsea career ending in acrimony, Conte insisted he would shake hands with the striker in future.
“I have no problem,” Conte added.
“We want to thank him for what he did with this club. We wish him all the best for the future.
“I’m not interested to continue talking about this issue. There is a lack of respect for my players because Diego is an Atletico player.”
Chelsea play at Atletico next Wednesday in Champions League Group C.
Chelsea play three games in eight days, with the Atletico game between Premier League fixtures with Stoke and Manchester City.
Only midfielder Danny Drinkwater (calf) and defender David Luiz, who is suspended domestically and has a broken wrist, are absent against Stoke.
Playmaker Eden Hazard is set to start in the Premier League for the first time this season against a Stoke side who have already beaten Arsenal and drawn with Manchester United at home this term.