Nothing I've seen or heard suggests to me that Vanuatu didn't submit the protest to the match commissioner within that two hour period.
Within two hours of the match commencing?
Or within two hours of the match finishing?
It's also notable that the same section, when dealing with eligibility protests for the final tournament, specifies that they need to occur no later 5 days before the tournament commences. You could then make an argument that the spirit of the clause is that protests over player eligibility need to happen before matches, not after (particularly since you don't want to encourage teams to continually litigate results based on paperwork).
Just added this para to a previous post, so pasting it here too.
It's also notable that the same section, when dealing with eligibility protests for the final tournament, specifies that they need to occur no later than 5 days before the tournament commences. You could then make an argument that the spirit of the clause is that protests over player eligibility need to happen before matches, not after (particularly since you don't want to encourage teams to continually litigate results based on paperwork).