@tekknj833 I’ve just tested this and yum list is correctly displaying the latest version of the package I upload. You could take a look in the primary.xml file to check that the version numbers listed are what you expect. You could also try using yum list available --showduplicates to show you all versions of available packages.
There is no way to clean up older RPMs when updated RPMs arrive. We are working on a new cleanup feature that will initially be able to delete by age and last downloaded time (likely to be released in the next version) and in a future iteration of this feature we will be adding “keep n versions of packages”.