Yes it is , like Federer's H2H with Stakhiovsky on grass is a stain on his legacy.
Who even brought up Federer? A very odd comment to make, and not analogous for many reasons (only 1 match on grass, Federer was in his 30s whereas Ferrer just beat Nadal while he's 31 and Nadal 27, etc.).
If you want to argue a stain on Federer's legacy just go directly to Nadal, which I would agree with.
Nevertheless, if Nadal manages to beat Ferrer today, which I think he will, he will do some damage control here since this is one of the most important tournaments after the Slams. Keep in mind that Ferrer has now beaten Nadal on hard court at both of his peaks on hc, and is 2-0 on hard court slams against Nadal.