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Published 23:25 17 Nov 2016 GMT
Updated 23:33 17 Nov 2016 GMT
Now both teams could face the possibility of a fine or even a World Cup points deduction.
"We can confirm disciplinary proceedings have been opened on this matter," a FIFA spokesperson said.
"Please understand we cannot comment further at this stage nor speculate on any outcome or provide an estimated timeline."
Martin Glenn, FA chief executive, has already said any fines will be challenged, Sky News report.
"If (FIFA) fine us, we'll contest," he said. "They have much bigger problems they should be concentrating on.
"I'm confident our legal position is right and our moral position is right. Our case is absolutely rock solid.''
It's not the first time something like this has happened. FIFA recently opened disciplinary proceedings against the Republic of Ireland's use of a logo to commemorate the centenary of the Easter Rising.
At club level, Celtic were fined by UEFA for flying the Palestinian flag to highlight the on-going Middle East conflict during August's 5-2 victory against Israel's Hapoel Beer Sheva.
The Glasgow side were found guilty of the charge for having an "illicit banner" by the European football governing body.


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