The Reapers only appeared in "Father's Day" because Rose created a paradox by saving Pete's life, and even then it sounds like they wouldn't have appeared if the timeline hadn't already been weakened due to two Ninth Doctors and Roses present.
Neither of those happened in "The Waters of Mars". For one thing, Adelaide pretty much reversed the Doctor's actions when she committed suicide; the only minor changes were that there were two survivors and that everyone knew why the base exploded. But even if she'd stayed alive, there wouldn't have been any paradox. And there was no weakening of the timeline, either.
And there seem to be good explanations for every other story.
In "Father's Day", the Doctor explained that when the Time Lords were around they had ways to keep them out of the universe, so they wouldn't have appeared in any of the classic stories (including comics, audios, etc.), except for some exceptions in the Eighth Doctor Adventures novels.
The only new-series story with a 'real' paradox and a weakened timeline is "The Sound of Drums"/"Last of the Time Lords", when the Master brought the Toclafane back in time to wipe out their own ancestors. But that paradox was protected by the Paradox Machine he'd made using the TARDIS, so there were no Reapers.
- ↑ There would have been a completely different problem—changing a fixed point in time—and we saw in "The Wedding of River Song" what that can do. But the Reapers don't seem to get involved in those cases.
- ↑ Gallifrey was destroyed in those novels, and there were paradoxes aplenty, and no Reapers. But it wasn't the same as the second time Gallifrey was destroyed. Instead of the Time Lords having no successors to take over, so the Web of Time deteriorated into a great big ball of timey-wimey, there were multiple factions fighting to succeed them. And presumably some of those different factions had enough knowledge and power to keep the Reapers away.
- ↑ As opposed to just an ontological/bootstrap paradox, like most of River Song's life.