When Pippi, Tommy and Annika hide in the well, all three sit in shoulder-deep water for several hours. Yet, when they finally climb out, the kids are bone-dry.
After Pippi rescues her father from his cell, there is still a shackle and chain attached to his ankle. Yet later when he is running down a paved walkway with the kids, the shackle and chain are gone.
In the English dubbed version of the film, it is obvious the characters are speaking in a foreign language as their mouth movements do not match the words that are said.
While the children are on an uninhibited island, they are seen finding and eating bananas. Bananas do not grow naturally in the wild, but must be planted and cultivated. And no indication is ever given that there were ever any human inhabitants on island.
At one point, the children crash land on an island supposedly somewhere in the South Pacific. Then the camera shows lions inhabiting the island. Lions are not indigenous to regions in the South Pacific, but are in Africa.
At one point, after the pirates have Pippi's father, one of the head pirates yells at his men to hurry and gather around before Pippi shows up. There's no way that the pirate could have known that Pippi even knew about her father's kidnapping since the pirates were not the ones who informed her of it. It was her father that informed her with a note in a bottle the pirates did not know about.