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The plugin only records 404s as determined by WordPress. They are 404s at the time they are reported, even if later they may be 200.
Based on your reply, I dug into my access logs. I noticed that the 404 errors were isolated to POST requests and GET requests were fine. Sure enough, when I turned on the column in the plugin’s report, I saw POST requests resulted in 404s and GET requests resulted in 200s. That explains why I couldn’t replicate the error. I’m guessing the POSTs are exploit scans or something and the 404 is WordPress or some security plugin stepping in.