I created a style to make it easier to modify all the text of the style at will. I wanted it to be compiled as if it were basically “No Style”, body text. But it compiles as H3 in MultiMarkdown. I have tried everything I could think of but am having no luck in figuring this out.
Put your cursor in some text, and check the Format ▸ Paragraph ▸ HTML Header Level submenu. If that’s set to anything but body text, the result should be self-explanatory. 
That’ll make headings in ePub, but we figured it would also make sense to allow for heading-level styles with Markdown output, too.
Otherwise, the only other thing that might do that is in the Styles compile format option pane. If your style has been added here as well, you can put a prefix and suffix around it (useful for making Markdown generators). If you don’t actually need it for that purpose, you can safely remove it from the list. With Markdown-based compiling, a project style with no matching style in this list will do nothing, and is thus a safe tool for editing roles, or other author-only semantics.
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Thanks! HTML Header Level was set to H3 for Body Text style. I spent hours trying to figure out where in my workflow the issue was. I should have asked sooner.