If I'm not mistaken, the Deucalion was stuck to the side of Saazbaum's landing castle right? How come on the Season 2 Episode 1 scene where Yuki rescued Inaho, they were underwater?
I figured out the answer myself. It's because it was a jump cut. The moment Inaho touched the Aldnoah drive, it had a jump cut to the present time where the Deucalion was underwater because they are docked at the beach where we saw Inko and the rest of the girls in bikinis prior. So it was just a jump cut that wasn't very clearly executed.