I understand the top comment as follows: The AIs were trained under one set of rules (remove obvious dead stones from your territory before counting) but are judged (in the paper) by another set of rules (if you have one opposing stone in your territory, that territory does not count).

Thus its no surprise that the AI can be attacked in this way: if you would apply the set of rules that it was trained with, all games from the paper would result in a (huge!) win for the AI.