Could be a number of issues here it's hard to say without the domain for your website. I recently installed a plugin on a site that little did I know added a noindex to my website and caused this issue. I was searching through everything as I had no message no manual action taken etc then I found out it was as simple as removing that plugin/editing it's code to remove the noindex it had automatically installed. Try and rule out all of the major causes first drop me a PM with your URL and I'll take a look see if I can get to the root cause for you. Best of luck!