This is quite a late response, but what follows is my understanding of what is happening. WeBWorK does not keep track of which scores have been pushed to the LMS. Consequently, it pushes every grade for every student to Canvas, sending the percentage scored on the assignment. Canvas calculates a new score based on the product of the reported percentage and Canvas's points possible for the assignment. If the score is different than what is recorded, it updates the Canvas database and posts a notification. If the calculated score is the same, then there is no update required.
So if Canvas has changed the score to 0 based on the Extra Credit setting, then Canvas is being instructed on this grade push to set the scores to zero.
So if Canvas has changed the score to 0 based on the Extra Credit setting, then Canvas is being instructed on this grade push to set the scores to zero.