The Chantry has often tried to stop the confusion between apostates and Maleficarum, and has spend many centries in doing so. However while some apostates may be classes as a Maleficer they don't need to be. The term Maleficer often denotes a mage who employs the use of a forbidden knowledge, such as a Blood Mage and the summoning of Demons, often the two are more than likely intertwined. The confusion may be caused apostates being hunted down by the Order of Templars, which often forces them to turn to such means in order to survive.
Originally the word Apostate only refered to those that had once been a member of the Circle of Magi and willingly left and the life path set for them by the Chantry. However now that the Andrastan Chantry is now the controlling religion in Thedas, naturally they assume that everyone born in Thedas is a follower of their faith. Anyone who disbands the laws set upon them at birth and leaves the Chantry is labelled as an Apostate.
This illegalisation of magic means that mages that belong to the race of the Dalish Elves, who practie a different form of magic to humans, have to hide their magic prowess from anyone who isn't Dalish, causing a higher level of tension between the Humans and the Dalish Elves.