My baby isn't feeling well and has spots on the inside of his cheek. What could be causing these spots? Is this serious enough to bring him to doctor?

Maybe thrush. If the 'spots" are whitish and don't wipe off easily, it may be thrush. If he isn't acting right, you should get him to his pediatrician for evaluation, regardless of whether it is thrush or something else. (thrush needs a prescription anti-yeast medicine, by the way.).
Thrush. The most likely cause for spots on the inside of the cheeks is thrush (oral candidiasis). This is a fungal infection. If your child is uncomfortable he/she needs to see the pediatrician to confirm the diagnosis and treat with an antifungal suspension. There are other causes of rashes inside the cheeks which are usually viral but are associated with other symptoms.