Ok, I had the same problem with autoSSL showing defective certificate on my subdomains. It has been solved by following the advise from the link from tmcstom that we should update everything on the server. Inside WHM interface, in the left column I simply needed to find and click on system update then software update and then cpanel update and then hard restart my whole server. I rerun the AutoSSL and it this time it went correctly and reinstalled the certificates and now all is green.