In The Witch's Familiar (Season 9, Episode 2 of the new Doctor Who), the Doctor literally said that "mercy" should not be in the vocabulary of the Daleks. Yet in the past at least one Dalek has said "mercy". The one I'm thinking about is The Big Bang (Season 5, Episode 13) where River Song got one to say "mercy".
As tilley31 points out in the comments, The Doctor has indeed heard a Dalek say "mercy" before. This is the first time he has heard it from a Dalek which is accused, by a highly unreliable source under emotionally charged circumstances, of killing his friend. A Dalek who, in general, is behaving in an un-Dalek like fashion. Something wasn't right, and that stood out for him just then.
Why then and not before? Before, it wasn't so relevant. Before, he didn't have the emotional distance to be as analytical: he was encountering his first Dalek since the war and what he believed to be his own act of double genocide. Before, he didn't have ready access to Davros's childhood, and a choice to make in that regard.
If we can dismiss the notion that this was simply a continuity error, and I think we can, since Steven Moffat wrote both "The Big Bang" and "The Witch's Familiar," then I think the answer has to be that the Daleks in fact never were able to say "mercy" before the conclusion of the latter episode.
If you recall, throughout this two-parter, both the Doctor and Davros remember the Time Lord as having abandoned child-Davros on Skaro ("I'm not helping you. I'm helping a little boy I abandoned on a battlefield. I think I owe him a sunrise"). It wasn't until the end of the second episode that the Doctor traveled back in time and rescued child-Davros in the hope of seeding the future killing machines with the concept of mercy, so he could clue his future self into the fact that Clara was inside the Dalek machine.
Therefore, the previous events related in "Dalek" and "The Big Bang" must have happened slightly differently before the Doctor changed the timeline, and thus the Doctor remembered them differently. What this insinuates about how the Doctor's encounter with Clara in that tunnel originally went doesn't bare thinking about.
In other words, timey-wimey wibbly-wobbly.
Let's think as a time traveler and answer this from an infinite time perspective. Davros made the Daleks after having seen that mankind was becoming and thought to make them indestructible since they are supposed to be the next evolutionary step. The Doctor is knowledgeable with all creatures and creations and was at the start and rebirth of the Daleks and was inside a sick Dalek and shared memories with one, rescued Clara from them numerous amounts of time, and had his identity erased from there data banks. It would only stand to reason the Doctor is also Multi specied. He was ONCE a Dalek and hated it and sought to have the memory erased and then reraised the Daleks to admit that they are a series in mankind's life and evolution even as an enemy,making him and his ability to save and Create Clara. In the new series he goes back in time to Davros and reprograms a word that is a code word for his Co created Daleks for an safe word for him and Clara, Mercy! The Doctor knows Davros is going to feed Them the Daleks his life story and this was the Doctor substituting for the word he removed from the Daleks which they knew cause he feed them his mind to the sick Dalek...HATE!