I agree that it is likely the food itself, not the fact that it is canned. If any of my animals eat just canned, we have no problems, but, they only get NV Instinct or Evo canned foods.
Keep in mind, too, that canned foods do tend to be higher in fat and that can be part of the problem - it's more likely higher fat content and/or poor ingredients are causing the problem.
Try introducing a different brand, but, do so slowly.
In regards to baking the food, the heat of doing such will destroy some of the nutritional content of the food.