As Clay retrieves the boombox to listen to tape 1, the cassette is already in the player. After he plugs the boombox in and touches a button, the CD lid opens. He closes it, opens the cassette door and it's no longer in the player.
On the bus Hanna put her number into Justin's phone but didn't take his number, later on he was the first to text her but somehow his number was already saved in her phone.
When Hannah tricks Justin and leaves him on the school bus, she is shown walking away and the bus is moving. The scene changes to Justin on the bus, and the bus is sitting still (note the trees in the background). When Hannah is shown again, the bus is moving again.
When Clay picks up the package left outside his house the package is poorly wrapped showing that it can be easily opened, but when Clay gets inside the package is perfectly taped up.
When Clay tries to get up from the ground after he crashes his bike, a film light (2K Arrilite with black wrap) rigged to a tree is clearly visible throughout the shot.