Hello, hope I’m not too late. I don’t check this forum too frequently.
Your problem seems caused by the feature: Change wp-content directory. This feature may strengthen your security but some plugins or themes may not working correctly after enabled it.
The best solution is to use other theme, as you can see the word “theme” is being mentioned in the error log. But if you don’t want to change to other theme, you can use this quick fix below.
Quick Fix
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1. Pay attention on the path after the “/wp-content“
2. In your example, that is “/theme/mytheme/favicon.ico“
3. Create the same directory path but starting with your new wp-content directory
4. For example: “/my-new-wp-content/theme/mythemes”
5. Copy the file to the directory (no. 4 above)
6. So it will become “/my-new-wp-content/theme/mythemes/favicon.ico”
It works on my cases. I have several (at least 3) plugins which are not working correctly after turning on “change wp-content directory” and I know it because I received 404 errors just as yours. Using the quick fix, the websites now are working correctly and no more such 404 errors.
The quick fix above is very useful to fix any theme or plugin which is not working correctly with Better WP Security feature: “Change wp-content directory”. I’ve proof it several times.
For your 2nd example, we will need to discuss more to see what is the source of problem.
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