First off, Kalonian Hydra's ability is not a triggered ability - is it a replacement effect, so it's impossible for it to be a missed trigger. In this case, Nina has allowed her opponent to commit a Game Rule Violation in not putting counters on his Hydra, and then progressed further in the game before alerting a judge. This is definitely a situation where an investigation for cheating would be warranted.
Either she was aware that the Hydra was supposed to get counters, and allowed her opponent to NOT put counters on it so she could gain an advantage, which would be cheating, and a DQ; or, if she legitimately thought that the Hydra's ability was a trigger and was just unclear on how the ability worked, it's Failure to Maintain, and we back up to when the Hydra entered the battlefield and put the counters on it.
EDIT: Ninja'd by Chris!
Edited Casey Brefka (Sept. 3, 2013 08:28:59 PM)