Plot hole: When Beast Boy finally brings himself to disable the Destruct-O-Tron, the hole he punches into the device to get inside is already visible when he is still bracing himself for the plunge. This background was simply reused for the scene where the device shuts down for good.
Plot hole: When Beast Boy hires at Meaty Meat, he takes away the ad "Human Help Wanted" from the window right next to the door, and when the Titans come by for a meal later on, the sign remains gone. But as the Nufu ship reveals itself and the restaurant clients panic, the sign is suddenly back in the same corner of the window, even though it is unlikely that the Nufu Source/Bob would take in more hired help and risk being discovered all too soon.
Plot hole: After the Titans have recovered their senses, they engage Mae-Eye and her gingerbread men. Just before Cyborg and Raven are trapped in giant jars, they blast Mother Mae-Eye directly from behind. But for her to enchant them, she just turns to her left and casts her spell to her side instead of behind her.