Files that execute scripts such as .pl and .php would show in the Apache log because they were attempted to be executed by a PHP handler, or specific handler like python.
This is considered a server error, so they would be recorded in the Apache error log because they failed to execute.
If I'm not mistaken; I do believe this is intended behavior.
Typically 404 errors are not server errors, so your standard files such as .gif or .html files would not show up in the Apache error log; they would show up in the access logs as 404's.
You can get the additional info to log to Apache error logs by modifying Apache configuration's 'LogLevel' to 'info' on servers that handle Apache 2.4
I'm not sure if this would be helpful, as there would be no mention of '404' errors in the error log -- you would just get something like
AH00128: File does not exist: /home/user/public_html/path/to/file
I would recommend opening a support ticket if you need assistance doing this; but I wouldn't keep it like this.