Some options combined with a large number of files can make scans take a long time, especially on slower servers. You can set a limit for how long Wordfence scans will run on your site. The option is called "Time limit that a scan can run in seconds." and it's available on the Wordfence Options page in the section "Scans to include". Leaving this option blank will allow Wordfence to use the default limit.
If your site reaches this limit during a scan, you will see a message in the scan results like:
Scan terminated with error: The scan time limit of 3 hours has been exceeded and the scan will be terminated. This limit can be customized on the options page.
If this happens, then the scan stops and reports the issues it has found so far, but the remainder of the scan will not be able to run unless you make some changes to scan options or the site's files. This issue will remain listed in the scan results until a successful scan has been completed without reaching the time limit.