I have many articles on my site revolving around the same keywords.
These are different articles, each having unique content.

Is there any known penalities or is it discourage practived to name the same keyword or keyphrases in duplicate folder locations?

.../sky/blue.php
.../water/blue.php
site.com/blue.php


note: I've review the moderator notes above and the repeat factor doesn't seem to be covered.

If you are referring to your duplicate file names in different folders, no there is no problem with that. It happens all the time with "index" or "default" as the root of various folders.