I just wanted to fix this problem but I can't reproduce it here. What exactly did you use as the file name? Was "Markdown" selected as the syntax definition in the File Information popover? For me, it works with spaces and other special characters in the file name.
I tried again (the file name was tumblr clients.md), but this time it worked fine! So I don't know what happened before (when it didn't work multiple times) but maybe a restart of my iPad since then fixed it?
Bugs
Sorry to be a bother!