Reasons for her departure are unclear, but the Mirror’s unnamed source is citing a “mutual” decision and careful planning, hinting that the change in the Time Lord himself, accompanying the rise of Peter Capaldi, an older and more serious Doctor, may be part of the change in dynamic. All the discussions about whether Coleman’s character would “flirt” with the new Doctor or not appeared to cause some embarrassment for the actress and perhaps the showrunners as well, given the obvious age gap between characters. Though the source is indicating that it’s a change in plot and tone for the series, one less appropriate to flirtation, it’s hard not to speculate that the dynamic has become less conducive to a young companion.
The BBC have not made an official statement on the subject, but the quotes provided by the Mirror seem rather authoritative. It would be a particularly large back-pedaling in the press if this announcement turns out to be untrue.