Re: http://amitmevada.com/category/Incoming/
Remove the category base from your permalinks. You can do that with a new rewrite rule or a plugin such as https://wordpress.org/plugins/remove-category-url/
Or, if you are using the Yeost SEO plugin, there is an option to remove category base from your URLs in that plugin’s settings.
Re: http://amitmevada.com/partial-incoming/
A guess — and only a guess — is that you have the posts in more than one category. For hierarchical URLs to work, your posts must only be in one category. So, if you are setting your posts to be in both the Incoming and, say, Partial Incoming categories, remove Incoming from the post and it should work.
This assumes you set up your categories with proper parent / child relationships, as you describe.