The M-Sport driver alongside rally leader Ott Tanak appeared to be incorrectly shown a red flag by marshal on Stage 17 after officials had declared the resumption of the stage.
The final test of the day was initially red flagged and suspended when fifth-placed M-Sport driver Adrien Fourmaux ran off the road.
Officials threw the red flag to allow recovery crews to remove the stricken Ford Puma that had partially blocked the road. Once the car was cleared the stage resumed allowing M-Sport duo Pierre-Louis Loubet, Breen, and Hyundai’s Tanak to complete the test.
However, a marshal during the stage issued a red flag to Breen and Tanak resulting in the pair reducing their speed for the remainder of the stage, sparking confusion.
“I feel sorry for that poor woman that had the flag out because god help her she has been stood out in the heat all day long, and she is probably going to get screamed at for holding the flag out,” Breen told WRC All Live.
“I genuinely, genuinely feel sorry for her, but these things happen.”
The FIA has confirmed to Motorsport.com that it is investigating the situation.
The overall classification has since been updated ensuring Breen will start Sunday 46.0s behind leader Tanak. Hyundai’s Dani Sordo will begin the final day in third 1m06.6s adrift ahead of Loubet, Kalle Rovanpera (Toyota), Takamoto Katsuta (Toyota) and Gus Greensmith (M-Sport).
Prior to the final stage, Breen had enjoyed arguably his strongest day in the Puma this season, and was the only driver to take a stage win away from Tanak on Stage 12.
The Irishman admitted that he felt much more “at ease” behind the wheel of the Puma having confessed to trying to overcomplicate his approach to recent rallies. Breen did have to contend with a hybrid issue during the day.
“Honestly, I'm really happy with how everything went today,” Breen added. “Our pace has been slowly getting better and better and I’m definitely feeling more and more confident with the car every stage I do.
“I’ve also learned the rally, and it is not what I’m used to. It has taken me a while to get into my head that you don’t have to be absolutely flat out compared the faster gravel rallies I’ve done in the last few years.
“I feel much more at ease with everything and I was trying to over complicate things in the last couple of rallies.
"We had a hybrid issue that was but hit and miss. I did some stages completely without hybrid. It was always a bit of a lottery if I had hybrid or not but the last two stages it rectified itself again."
While Breen has led the M-Sport charge team-mate Loubet has produced his best display in the WRC to date to hold fourth.
“I’m happy to be at the end with no mistake and we did our best,” said Loubet.
“The pace was there in Portugal and from the moment we got in this car everything was better so let’s continue.”
M-Sport has since confirmed Fourmaux's car won't return to action on Sunday.
