I saw those. Thought they were intentional. Due to minor incompatibility between most word processors and other words processors (including the one on this site), you will generally get quirks like that.
Whenever I use indented paragraphs in my Word documents (e.g. the cardinal's phoney suicide note) those require me to manually go back into this site and manually indent them.
Try to avoid manually formatting anything in your master files, if possible. Use styles instead. That way you get fewer magic hidden characters copied over that the site doesn't know how to process.