[Plugin: Better WP Security] Too many file modification warnings and 404 errors

I’m guessing you’re using some sort of caching or something similar that is writing to the file system and causing the file change errors. Try excluding the files in the Intrusion Detection settings in Better WP Security.

As for the 404s, are they really strange files that make no sense or a lot of images, css files, etc? The former probably means something was scanning your site (still not necessarily a bad thing) and the latter means there are a lot of bad links in your code or in sites linking to yours.

Today, all of a sudden, I got over one hundred of 404s errors in Better WP Security log
The UPI is /not_found?ver=3.4.2
The IP addresses come from all over the world.
I checked my website, there are no bad links at all.
I wonder is it because I selected “Remove WordPress Generator Meta Tag”?
Or some bots are trying to scan my site?

That does sound like a scanning issue after something was updated (many items will attach the version string which can get confusing. Try re-adding the generator meta tag and see what happens.

I am experiencing the same problem, over the last several days, I get “Your database contains 2923 404 errors.”

For example
2012-12-12, 9:19 PM 209.239.114.234 /browse.php/Phm0gx5V/Ca81x9n9/juKOe5Db/uHdwYVcD/mHOS_2Ba/MOvKyAbA/jfInq_2F/GddfPlUm/FGurlv4L/hNyp07ai/nAvlD3YZ/oD0smfVL/b13/

2012-12-13, 11:42 AM 66.249.73.182 /shop_order_status-sitemap.xml

2012-12-15, 10:26
130.216.147.183
125.239.115.181
119.224.136.105
49.224.106.186
49.224.237.191
216.232.179.143
49.224.237.192
49.224.237.196
125.236.236.227
49.224.237.197
49.224.252.176
49.224.252.177
203.118.149.40
58.96.79.103
121.74.49.65
182.54.161.10
210.55.255.107
125.238.26.63
etc

I checked all my links and none gave 404 errors
I don’t understand what is happening.