When the Bongo bobs out of the water at the city of Theed, you can see a speeder boat in the background far in front of it. When you next see what's in back of the Bongo, the Speeder's right next to them, and almost behind them. Also, the swans have returned. I guess when they saw stupid Jar Jar pop out, they felt it was alright. If you don't believe me, watch it again and again. It may look like the Sub continues to move in the shot where it pops out of the water, but the shots from the inside clearly show that it's stopped.