When Babu accidentally split himself the first time, he was split above his red stripes, but before he put himself back together, he was split below the stripes.
When Scooby gets away from Jadal, Babu's vest is briefly missing.
When Shaggy is swimming in the pool, his shirt has long sleeves.
When Henry uncovers his head after Jeannie came into his and Corey's room, he's wearing a shirt that is the same color as his hair, instead of two shirts that are different shades of green.
In the last scene when Fred says "Don't you guys ever learn?", he speaks with Henry's voice.
When Babu attempts to show Scooby, Shaggy, and Henry that he can travel through walls, his lips don't move when he says, "Yapple-Dapple!"
When Henry is getting ready for bed, Corey says "Good night" to him. Henry's is also saying something, but nothing is heard.
When they're looking for a secret panel, Henry speaks with Abin's voice.
Although purportedly taking place in Persia (an archaic name for Iran, still used poetically), the topography is clearly Arabian or Egyptian. Another aspect of this is that the king is called a Sultan, whereas the Persian analog would be Shah.
Corey didn't know what happened with Henry and the mirror and didn't believe him, but he was watching Henry and the mirror Henry.