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How is is possible?
Subfloor installed when basement subgrade was soggy. Basement generally has many walls and few windows - perhaps windows on only one side, so limited air movement. Mold starts.
Remove the mold with bleach and as long as you kill it, it should not come back if you have removed the source of moisture and have the basement humidity under control.
Don't use bleach on mold. It won't work and will potentially make the problem worse. This is a common mistake people make and it is propagated on the internet and other places. Bleach will kill bacteria, but it doesn't kill mold spores, which is how mold propagates. Using bleach on porous materials only gets the top surface, but doesn't penetrate down into the material where the spores tend to be. The Advantech is wood based, and organic materials neutralize the bleach, further making it ineffective. Additionally, the bleach kills the 'beneficial' bacteria that feed off of mold colonies, which is why using bleach can make the problem worse.
You should use a product designed specifically for removing mold and there are a number of products available from Lysol, Mold Control, etc. You can also use Borax if the nasty stuff isn't your cup of tea.
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This is one of many reasons I try to design houses without basements or crawlspaces. Getting the building envelope "dried in" should be a top priority. Prefabrication (roof trusses, panelized construction) reduces the time before dry-in. If you do take on water, use large fans and/or dehumidifiers to dry the space out ASAP.
Advantech is amazing stuff but it's not mold-proof; when the temperature is in the 50-80° range and there is a source of moisture, mold will likely develop, it's just a matter of time, so remove the moisture source quickly.
You don't. It's almost impossible to avoid in some climates which have high levels of dampness and constant precipitation.
The reality is that some mold isn't a big deal if the home remains dry and the mold is encapsulated. Conversely if one is so inclined they can clean it off.
Three primary actions can reduce the probability of this happening:
1. Do not install subfloor when the basement or crawl space subgrade is wet - delay framing until if is dry and there are a few days of dry weather to complete framing. As a practical matter, this also means delaying the framing of the subfloor, because the framing will block sunshine and delay the drying, and because your framers won't want to mobilize twice. Once the Advantec is installed, far less water gets through to the space below.
2. Use a product like Zip sheathing for the roof decking and tape it off. Properly taped off it will prevent 95% or more of water intrusion and keep the subgrade dry.
3. Manage moisture in the crawl/basement even after the above two issues, so put a dehumidifier down there, install the perimeter footing drain ASAP, etc.
I don't think the guarantee covers this, my recollection is it covers swelling and disintegrating.
Mold can grow on anything. In a marine climate I've seen it grow on plastic, stone, steel even glass. Mold is pretty easy to deal with once the water source is removed, if washing with TSP doesn't get it all then encapsulate it with primer.
I'd also be worried about the framing warping if things are that wet.
Just clean it and move on.
Btw, newly built homes contain a lot of moisture and it's going to take some time for it to 'dry out" so good idea to run a dehumidifier for a while.
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In that case don't remove the sheetrock and insulation. The mold will go dormant due to a lack of moisture and stay encapsulated inside the ceiling.