Is there any harm in stirring boiling food with metal spoon? i recently was cooking nacho cheese and stirred/ left my metal spoon in the pot while boiling said food?

No worries: I suspect the pot is metal too. There is no risk from metal eating utensils contaminating food. These types of items are made with materials that will not contaminate food by both design and the law. Be careful scraping non-stick coated pans with the metal spoon however since the metal spoon can chip the Teflon coating. But even if those chips get in your food it wont harm you, just your pan.

Safe: Modern utensils are made with food safe metals and will pose no problem when used for cooking, eating, etc. (even if left in the pot) If for some reason you are using an antique spoon, there may be the chance of lead. Otherwise, you are safe.