Bug in code

In the function apt_generate_post_thumb, you have the following code:

//Fix for checking file extensions
$exts = explode(".",$filename);
if (count($exts)>2)return null;
$allowed=get_allowed_mime_types();
$ext=pathinfo($new_file,PATHINFO_EXTENSION);
if(!array_key_exists($ext,$allowed))return null;

You check if, for instance, jpg exists as a key in the array retrieved from get_allowed_mime_types. The problem is, it doesn’t. The key for the JPEG MIME type is jpg|jpeg|jpe. Thus, your plugin thinks jpg is not supported.

Additionally, a few lines later, you do this:

// Get the file type. Must to use it as a post thumbnail.
$wp_filetype = wp_check_filetype( $filename, $mimes );

extract( $wp_filetype );

// No file type! No point to proceed further
if ( ( !$type || !$ext ) && !current_user_can( 'unfiltered_upload' ) ) {
    return null;
}

The function wp_check_filetype checks if the extension is valid AND allowed. The difference is, it does it properly. You should replace the former broken code with the latter:

// Get the file type. Must to use it as a post thumbnail.
$wp_filetype = wp_check_filetype( $filename );

extract( $wp_filetype );

// No file type! No point to proceed further
if ( ( !$type || !$ext ) && !current_user_can( 'unfiltered_upload' ) ) {
    return null;
}

file_put_contents($new_file, $file_data);

// Set correct file permissions
$stat = stat( dirname( $new_file ));
$perms = $stat['mode'] & 0000666;
@ chmod( $new_file, $perms );

// Compute the URL
$url = $uploads['url'] . "/$filename";