First, I would still not say "0 is not a multiple of 9 and 12" but rather "0 is not a positive multiple of 9 and 12" in my explanation of the problem. I'm surprised that Singapore Math doesn't just say "the smallest positive number" as this definition would be mathematically correct regardless of whether you assume negative numbers have been introduced or not. However, I don't have a copy available to check for myself.
Second, I still do not think that excluding 0 is defensible. It states that "both trains have just left". It does not state that the station has just opened. If, in your hypothetical explanation of the problem, we are at 36 minutes, then 72 minutes later will be 36 minutes from now.