Sometimes I re-positioned, and sometimes I didn't. With my son, I had to watch his circulation (he had heart probs when born) and so if he was lying on his side with his arm twisted under him, for example, I'd pull his arm out a bit. Also, if they had legs/arms stuck through the sides of the cot slats I'd pop them back in too

But other times (eg bum up head down etc) I'd just leave them be. At that age they start to work out what's comfy and what's not, and usually shuffle themselves around if they feel uncomfortable.