It is possible to measure these compounds on GCs and HPLCs, but it's expensive. At the start of the process, reduce the amount of simple sugars present, which will reduce bacterial and yeast growth, and increase chunky materials to increase the ease with which oxygen can diffuse into the material. It doesn't matter if anaerobic organisms are present, as long as they aren't growing. Because VOAs, alcohols, and phenols produced by anaerobic bacteria and yeast are very toxic to the roots of plants. Very small quantities are phytotoxic, that is, they kill plants.
Aerobic organisms consume VOAs and alcohols.
Think of bacteria enjoying champagne or other alcohols, just like humans. Of course, alcohol has a toxic effect on aerobic bacteria at high concentration, just like humans, but eventually, the alcohol, VOAs and phenols will get eaten, and the phytotoxic effect will go away. Phenols are hardest to get rid of, because they are more difficult to decompose. But, given time, aeration and the growth of aerobic organisms, any amount of anaerobic by-product will disappear. Again, your nose is a good way to tell.