I had the same problem, my site that was getting this message in the dashboard:
“Your homepage cannot be indexed by search engines. This is very bad for SEO and should be fixed.”
This message is actually from the WordPress SEO plugin by Yoast. I searched the forums and found several people who were getting the same issue, and who were able to rectify it by visiting the Yoast widget in the dashboard, and clicking the OnPage.org “Fetch again” button:
https://www.ads-software.com/support/topic/updated-and-now-it-says-homepage-cant-be-indexed
https://www.ads-software.com/support/topic/your-homepage-cannot-be-indexed-by-search-engines
However, there are several people who were unable to clear the message, and I found myself in the same situation. I was about to write off the error as erroneous, when I decided to check the headers using several different tools on a couple of different sites. When I did, I discovered that the site was actually returning a 503 Internal Server Error to bots, and when I went through the access logs I realized that it was doing the same to Googlebot as well.
I disabled all of the plugins and re-tested, and the error went away. I then re-enabled them all aside from Wordfence, and it stayed away, but as soon as I enabled Wordfence all of the bots, including Googlebot, were blocked again:
74.125.18.224 – – [27/Nov/2015:00:21:06 -0600] “GET /robots.txt HTTP/1.1” 503 2438 “-” “-“
74.125.18.224 – – [27/Nov/2015:00:21:06 -0600] “GET / HTTP/1.1” 503 2438 “-” “Googlebot/2.1 (+https://www.google.com/bot.html)”
I verified with ARIN that those are indeed Google IP addresses. I have no idea why Wordfence has started blocking Google IP addresses, but this will kill your seo dead if it is happening to you. Also, there are 0 IPs showing in the “Blocked IP” list, so these appear to be blocked by default and not blocked due to bad behavior.
After disabling Wordfence I was able to also successfully use the Fetch Again button in the Yoast SEO widget, and OnPage.org was able to verify that the site was visible.
Problem fixed.I hope it works for you guys too.
https://www.ads-software.com/plugins/wordfence/