What kind of a query are you running? All the normal queries using pure Dataview only handles .md files by default. So if you’re using javascript to read all the files, then you also need to use javascript to limit your query.
So please present your query so we can further help you investigate what’s happening. (And if you enclose the entire query (and/or example data) within four backticks, it’ll present itself nicely here in the forum)