Guardiola was warned about the issue twice in mid-December and now faces disciplinary action for "wearing a political message, specifically a yellow ribbon".
The kit and advertising regulations referred to concern players and club officials in the technical area.
Starsport understands Guardiola could also request a personal hearing to challenge the charge and is reluctant to back down.
The Football Association has now brought a charge against the 47-year-old, who Press Association Sport understands has ignored two previous warnings from the governing body about the matter.
The report claims that the charge was then triggered during City's shock FA Cup exit to Wigan Athletic on Monday, where once again the ribbon was visible.
Puigdemont served as president of Catalonia up until October 2017 when he led a referendum on Catalan independence from Spain that was declared illegal. So, while they are not out, always here (points to ribbon) will be shared with me.More news: Palestinians slam USA embassy Jerusalem opening as 'provocation'
Although Guardiola acknowledged that simply playing attractive football is not enough and he will be judged on silverware.
The serial winning coach struggled somewhat in his first season in England, with his side finishing in third place in the Premier League.
City have produced some of the best football in Premier League history this time round to earn plaudits from around the world.
Guardiola, who has landed 22 major titles since becoming a boss, said: "We have to lift titles to give more value to what we have done".
"If the rules allow us to do that, he is a free citizen", Mourinho said.
"Of course we'll be judged on it, this is a club that needs to grow up every year and win titles, now we have [the chance to win] the first one". Hopefully on Sunday we'll have the first one. "My family saw it, they saw the police searching the plane, and that's it".