I installed the latest stable version of wordpress & the plugin
WP Security Scan & it's telling me to fix the following two errors.

Your table prefix should not be wp_. Click here to change it.

The file .htaccess does not exist in wp-admin/.

I changed my permalinks to /%category%/%postname%/ could that
be causing some of the errors anyway how do I fix these two errors.

I met the same problem before, asked so many people and didn't find the solution, thanks the back i made. After that i didn't install any plugins related to database. BTW, the plugin has give us some clue before we install it, "Make a backup of your database before using this tool". LOl~

Your table prefix should not be wp_. Click here to change it.

This is not really an "error", just a suggestion. It is just an extra security measure since all hackers would know that most Wordpress databases start with wp_*. Wordpress allows you to change this prefix to make it more difficult for your site to be hacked. I'd be willing to bet 95% of WP sites just leave it at "wp_" (the default) but you can change it if you want.

The file .htaccess does not exist in wp-admin/.

As this article mentions, there seems to be some errors with WP 3.0 with this plugin. The htacess error the plugin is referring to will deny random access to the admin files.

I would search "wordpress security tips" and you'll find tons of great articles on things you can do to secure your blog.