When Maya's brother is helping her recover after killing the coyote, we can see Maya's black tears turn clear in a closeup. The camera cuts to a two-shot and the tears are black again, then back to the closeup where the tears are again clear.
In the scene where Hiro is knocked out by Kensei/Adam, a goat comes to lick Hiro, and you can clearly see oats under the collar of the shirt of Hiro.
After The Battle of Twelve Swords, when Hiro and Eriko are riding away - you can see an empty plastic drinking bottle in the grass. (at around 18 mins 46 seconds)
Matt Parkman and Detective Fuller claim that Angela Petrelli's fingerprint was found on Kaito Nakamura's picture. However, she was wearing gloves when she handled the picture so she could not have left a print.