In halo contact harvest it was clear that humans where forerunners but in more recent halo stuff they are aliens. Why did 343 change this and does it mean that contact harvest is not canon?
No, 343 Industries did not change anything in this regard. Bungie originally planned for humans and Forerunners to be the same, but that changed during the development of Halo 3. 05-032 Mendicant Bias might have interpreted the reclaimers on Harvest to be living Forerunners because he was not aware of the geas that the Librarian had given to humanity that would allow them to use many forms of Forerunner technology, among other things. Or alternatively, he saw humans as his makers because they actually were:
http://www.haloarchive.com/the-library/mendicant-bias-forerunner-in-form-human-in-essence/
You should ask Bungie since they were never very consistent on just what the relationship between humans and Forerunners was.
Bungie had purposefully left the relation between Forerunners and Humans ambiguous. Closest thing we got was when Guilty Spark told the Chief “You are Forerunner”; but what is generally accepted is that he meant that figuratively, not literally; that Humans were the inheritors of Forerunner legacy, and were essentially filling in the role of the Forerunners.
343i expanded on this mystery and gave faces and origins to the Forerunners. As for the Contact Harvest thing, Mendicant Bias called the humans his “makers”, but it was the not-yet Prophet of Truth who called them left-behind Forerunners.