When The Doctor whisper in River's ear, he clearly says something very short - only two syllables. Later, when it's revealed what he had said, it's a whole sentence with five syllables.
The marks appear on The Doctor's forearms but he has nothing to draw them with.
When River Song and The Doctor arrive to the "timey-wimey distress beacon", the star field and dusk behind them "twitch" quite violently.
When the gang are at Lake Silencio, there's a moment where someone is visible behind the hut behind The Doctor's car. Their features aren't visible, but their moving silhouette is.