"I accidentally manually submitted the url to google and manually in submitted it to index and that when this issue began...."

It sounds like you accidently added this URL to the index. You can follow the procedure outlined below to request Google remove the specific URL from the index:

https://support.google.com/webmasters/bin/answer.py?hl=en&answer=59819

I checked your site's structure using Screaming Frog and it does not appear that you are linking to any non-.html versions. If I perform a scan using one of your non-.html pages, it appears that it only links to itself.

Since you have the 301 redirect in place, you can choose to wait it out and Google should correct things eventually; otherwise, requesting Google remove the URL is a faster... PERMANENT process.

Good luck.

Mike

It all depends whether it makes sense for your business.

For instance if you sell shoes, you would probably not benefit from having an Armani microsite and a Nike microsite UNLESS you want users to assume you ONLY sell Armani or ONLY sell Nike.

The company I work for uses microsites, because our main site is just too generic. We sell software and our software can be configured for any industry, but to say that can deter some people. So we have our main site (just examples here) software.com and microsites food.software.com, jewelry.software, animal.software.com - this approach works for us, because we have slightly different solutions for each of these industries and we do not want to look too generic or single people out if we listed these on our main site.

Some of it has to do with SEO, but really think about it from a marketing standpoint and how you want to market to your visitors. We want to market to visitors with a microsite saying, "We have awesome food software" instead of saying with our main site, "We can tailor your software for the food industry".

It has worked great for us having microsites. It is a little more work, because you need to manage multiple sites and have unique content across multiple sites, but we are seeing really good returns.

Hope this helps.

Mike