In the scene where where the super six kids first see Jadoo, one of the kids (Hansika Motwani) is missing. Later in the song, the entire super six group is present, including Hansika Motwani who wasn't present earlier.
When Nisha takes Rohit to the club to meet her friends, he is wearing a blue-checkered, half-sleeved shirt with black suspenders. After he starts singing outside after the rain begins to fall, you can see that he now has an off-white t-shirt underneath his blue shirt and proceeds to wear it all throughout the song.
When Sanjay Mehra first receives the extraterrestrial signal, the floppy drive doors on two of the three drives are open in one shot, then closed in the next shot.
Hrithik's hair changes in several scenes.
The whole movie is based upon sending various sounds in space. But the fact is sound cannot travel through space. Thus the signal sent cannot reach to the aliens.
The alien Jadoo uses sunlight to gain energy but in one scene Jadoo drinks cold drink.
Realising his son's almost incurable disability, a disheartened Sonia Mehra (Rekha) plays her husband's tune (which he had created to contact the extraterrestrials) in the musical keyboard. But in reality, the keys she presses will not generate that tune. It'll instead generate the song Pardesi Pardesi from Raja Hindustani (1996). Both the tunes are different.
The car crash scene supposedly takes place in Canada. But the Volvo the couple is driving is revealed, briefly, to have a Europe/Asia style of license plate, not a North American style plate.