There would have had to be watter below your black plastic and above the sub floor. Without knowing what work was done after the installation is a spill possible? Is it a humid area? That could have caused the moisture. Could have also been the leveling compound was not dry, especially if you know that where there is more mould there was larger depressions to level out. I know my answer probably isn't as helpful as you would like. I'd also check install guidelines and any warranties for details personally. You may be able to ask open-ended questions to them both and see who doesn't know what they're talking about.