The manuscript format will interpret empty lines as section/scene breaks by default. The question is whether they are supposed to be breaks (and then you probably just want to leave it alone as this is a pretty typical way of marking a break, unless you’ve been requested to use something else), or if maybe these are accidental double-returns worth cleaning up?
As for the numbers, it’s difficult to say, but maybe you have “phantom” list formatting in your document in areas. I would select any lines that have numbers like that, in the editor, and set Format ▸ List ▸ None. This can sometimes happen with text pasted from other sources as a starting point.