I was having this problem: When I tried to convert a web page to some other file type, It just reproduced the web page, as a bookmark.
This was the same whether from the web browser, when I share from Safari or by using >Data>Convert
It was doing this with every web page, even Devonthink’s own: PDF, MarkDown, Rich Text … it just kept making identical web bookmarks.
Solution: Quit and Restart Devonthink.