I watched supersize vs superskinny last night and the skinny guy on it was eating 1300 calories a day which the doctor said is the recommendation for a 3 year old boy and is not safe (and showed pictures of malnutrition diseases), but I eat 1200 calories and I thought this was quite common on diets but am I doing myself harm??

no you're losing weight, the doctor I presume was talking about maintaining which is completely different. the skinny guy was eating so few calories he was losing weight, which when you're already underweight isn't a good thing. Don't worry about it, you're okay.

There could be a number of variables. First of all, men need more calories to maintain (unfair, I know). I'm not sure of that man's height or how much weight he was supposed to have on him in order to be considered healthy. So perhaps 1,300 was far too low for him. That's no reason to think it's too little for everyone.