If you work out of Ontario as per your employment contract, the company shouldn't be deducting taxes for Quebec. They should be deducting for Ontario instead. You don't have to worry about this as the company's payroll department should handle this appropriately. Consult with a tax lawyer if you want further clarification on this, not an immigration lawyer.
As far as immigration and residency rules go, this is clear as day and you're perfectly fine. There is no rule that prevents you from working remotely from Ontario for a Quebec based employer.