Need A Little Google Seo Advice

When google indexes one of my new sites, they seem to come up with a lot of extra pages, that don't really exist. They will list the pages that are really there, but then they will list an extra home page like "mywebsite.com/mywebsite

Then there will be pages like "mywebsite.com/basketballs which is ok, because it exists, but then they will list "mywebsite.com/caterories/basketballs which as far as I am concerned does not exist.

I also link to amazon for some products I sell, but I use a link cloaker so the affiliate link is not in the content of the page, but somehow google indexes a page that has amazon information at the top like, Great Deals At Amazon, which if clicked goes to amazon, then something below it about my content, and then the domain name of mywebsite/the page the links are on.

I do only blogs, and use the flexible2 theme.

My question is, when you put in site:yourdomain.com to see what google has indexed, there is a box next to each page result that says remove this result. If you remove the ones that should not be there, is that permanent, or will they just show up again.

Also is there any reasons not to remove pages you don't want indexed.

Thanks Glenn