By default, Alfred searches a subset of files to keep things clean, and md isn't one of those types. If you'd like to include that file type in Alfred's default results, you can click on the Features > Default Results > Advanced button and drag the md file into the user-defined types there.
I always recommend to have less stuff in your default results and separate file search to the [spacebar] prefix which keeps the default results focused, clean and fast.
Cheers,
Andrew