Sounds to me like you have your entire manuscript double-spaced manually. Since an empty line between a sequence of paragraphs is generally considered to be a scene break, Scrivener’s default settings assume that if you leave an empty line, you want a scene break. If you use a compile format (like Manuscript) where the standard for denoting a scene break is a hash, then you get a hash between each paragraph.
So how you fix that is up to you. Generally the best answer is to write paragraphs in sequence with one another, as that is the standard style for using word processor writing environments. One could also switch to a different compile format that doesn’t denote scenes in this fashion, though. Or modify the manuscript format to not denote scenes with hashes, etc.
Meanwhile, here is a list of previous discussions on the matter: