Samus has been involved in two controversial "rSFF" matchups
Reverse Same Fanbase Factor (or rSFF for short) is the theory that the "weaker" of two characters (using indirect statistics) can sometimes overperform in or even win a matchup by dominating the voting block shared by the two opponents. The idea behind rSFF was first brought up during the Summer of 2004, when it was suggested that, because the Chrono Trigger fanbase prefered Magus to Crono, the wizard would be able to rSFF his way to victory. He did not and appeared to have gotten SFFed normally.
Though the debate is still out regarding the existence of rSFF, some claim its first proven case took place in 2005, when Samus, a character who had outperformed her Nintendo counterpart Mario indirectly in two of the previous three years, was nevertheless crushed by the Nintendo icon in a direct matchup (Mario earned 59.79% of the vote).
In 2006, Snake's Brawl announcement is generally given credit for his great run and he appeared to have a good chance at winning the finals, but Samus, who had looked vulnerable in a few previous matches, defeated him with 53% of the vote, leading some to speculate that Snake's Brawl announcement support collapsed against actual Nintendo characters. In other words, rSFF.
rSFF need not actually result in the stronger character losing. In 2004, Mega Man went up against Zero, the sidekick from the Mega Man X series, and surprisingly was held to just over 56% of the vote, over 13% lower than the Oracle expectations and nearly 4% lower than even the extreme low end of Oracle predictions. Proving this was no fluke, Zero met up with Mega Man again in 2008 and LFFed him into losing a close match against the Weighted Companion Cube, whom he'd solidly beaten the previous round. Although the 38.44% that Zero scored on Mega Man directly in this match is more in line with expectations in a match with no SFF, characters tend to get SFFed even worse in 4way matches if there's any risk of the "stronger" character losing, and Zero didn't roll over and allow Mega Man through. Given that the Mega Man X series beat out the classic Mega Man series in a "Favorite Mega Man Series" poll, it's extremely likely that Zero was rSFFing Mega Man both times.
2018 arguably had the first effective case of rSFF when Tifa Lockhart beat Sephiroth: Sephiroth, as the antagonist of Final Fantasy VII, was always one of the strongest characters in contests, while Tifa, in spite of being the most prominent female character in the game, is not the most famous (she only debuted in the fourth contest, while Aeris, subject of a famous plot twist, was there in the first Character Battle). Seph caused Tifa's elimination in 2008 and handily beat her in 2010. But in the loser bracket, Sephiroth, who had already been proven as decaying in the previous contests (not to mention the very previous match, where Mario beat him with nearly 60%), was surprised by Tifa, who got the win with 52.33% of the vote.