Dangers like that can be identified quite easily. It's a qualitative thing, and qualitative chemistry is pretty robust. For instance, we can say that there's a risk that a particular reaction will produce hydrogen under specific circumstances. We'll just build the plant accordingly instead of trusting that we can always operate the plant correctly. Sooner or later, you'll end up running the plant in the wrong way, and you'll produce some hydrogen, so it's good to have a plant that can detect and deal with it safely.

However, usually the idea is to produce something entirely different, and do so efficiently. Those sorts of questions are quantitative, and that's where things can and will go wrong all the time. Like, how do you ensure that your expensive catalyst isn't covered in goo, or corrosion doesn't eat your fancy impeller? How do you ensure that the amount of impurities in the product will remain reasonably low? It's all about the quantities and reaction rates, and that's the hard part with inorganic chemistry.