Does Wordfence scan the uploads folder/directory

Hi,
Yes, a regular Wordfence scan includes the following:

• wp-admin directory
• wp-content directory
• wp-includes directory
• All sub-directories of the above directories.
• All files in your base WordPress directory

If you are sure that “Scan file contents for backdoors, trojans and suspicious code“, “Scan file contents for malicious URLs” and “Scan image files as if they were executable” options were enabled and you didn’t exclude “wp-content” or any of its sub-directories in “Exclude files from scan that match these wildcard patterns” option, then please email these files to “samples [at] wordfence [dot] com” so we can investigate these files.

Thanks.