As we see under the MTR 4.2 Tournament Shorcuts, “A player who casts a spell or activates an ability that targets an object on the stack is assumed to target the legal target closest to the top of the stack unless the player specifies otherwise.”

As Magic players, we all know it is clearly the tactically correct choice to counter the original spell, rather than counter the counter. And this is doubly true when it’s a counter with a big downside like Pact of Negation. So, while we should probably ask Arthur a couple questions to make sure nothing fishy is going on, it is very likely that he simply assumed that it was so obvious he would make the overtly correct play that he didn’t need to spell it out for Neil.

However, as judges we do not assume that players are making tactically correct choices. We assume they are adhering to established shortcuts. And it is exactly to clear up this sort of ambiguity within a counter war that this particular shortcut exists. So Mana Leak counters Pact of Negation, there is no infraction, and Arthur learns a valuable lesson about stating the obvious.