Portuguesa used a suspended player against Gremio, which could see them deducted four points and relegated insteadFluminense could be spared relegation after it Portuguesa may have played a suspended player.
Flu were the reigning Brasileiro Serie A champions but were relegated on the final day of the season on Sunday, though it now appears they may get a reprieve.
Brazil's superior sports justice tribunal (STJD) will make a ruling this week, after Portuguesa brought on midfielder Heverton in the final minutes of Sunday's 0-0 draw with Gremio.
Heverton received a two-match ban last Friday, and the lawyer representing Portuguesa at the court informed the club that he had only been banned for one match, which he had previously carried out.
The official announcement from the CBF (Brazilian Football Confederation) regarding the two-match ban was only released on Monday - after the end of the season.
If found guilty, they would be deducted four points, relegating them instead of Fluminense.
That is not the only controversy to have dogged Brazil's top league this week, however.
Vasco da Gama, who lost 5-1 to Atletico-PR after the ugly violence at the Arena Joinville, are claiming that, according to the rules, the match should not have been suspended after over an hour had been played (it was stopped after 71 minutes).
Because of this, the club are arguing the game should have been cancelled, with the result altered to 3-0 win in favour of Vasco instead, subsequently saving them from relegation.
Finally, Flamengo could end up losing four points for using Andre Santos in a match where he also should have been suspended.
If Portuguesa are not deducted points or if Vasco earn a reprieve, Flamengo may end up being relegated instead.