You have WordPress Debugging turned On / Set to true in your wp-config.php file. More specifically if you use/set define('WP_DEBUG_LOG', true);
to true then WordPress will use the default WordPress Debug log in the wp-content folder to log errors. /wp-content/debug.log to log all errors. BPS intentionally allows this to happen and will not override this default WordPress Debugging method and force errors to be logged in the BPS php error log instead of using the WordPress Debug log. On a Live Production website you would use Debugging to check for any issues/problems/errors and then turn Off Debugging as soon as troubleshooting is completed. You do NOT want to leave WordPress Debugging turned On all the time on a Live Production website.
Note: There is actually a minor bug with the hud-dismiss-functions.php file on line 450, but it is a very insignificant issue that will be fixed in the next version of BPS Pro. It does not adversly affect anything and is just a PHP Notice error.
define('WP_DEBUG', true); define('WP_DEBUG_LOG', true); define('WP_DEBUG_DISPLAY', true);
So anyway all you need to do is turn off WordPress Debugging in your wp-config.php file and all of the things you have mentioned in your topic post will go away.
Anytime you are manually modifying website files you need to follow these AutoRestore manual file modification procedural steps when manually modifying website files or you can just choose to restore the wp-config.php file from Quarantine when it is quarantined by ARQ.
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/
AutoRestore/Quarantine Correct Usage
AutoRestore/Quarantine (ARQ Infinity) IDPS is a real time file monitor that monitors all of your website files for any changes. When manually uploading files with FTP or modifying files or folders on your website follow these simple procedural steps for AutoRestore/Quarantine (ARQ) to avoid having those files autorestored and / or quarantined. If files are sent to Quarantine then use the Restore File option in Quarantine to restore those files. ARQ is amazing, but it cannot tell who you are if you are manually modifying files or folders outside of your WordPress Dashboard – that is not possible.1. Turn ARQ Off.
2. Upload or modify files or folders on your website.
3. Click the appropriate Backup Files button: Root Files, wp-admin Files, wp-includes Files or wp-content Files Backup Files button.
4. Turn ARQ back On.