The latches/handles on the side window are glued on by the window manufacturer and have come off on a few boats. Glue it back on with the same glue used to hold on rearview mirrors (available at any autoparts store).
As to the water intrusion, it's either coming from a frame that's not completely sealed around the opening or from between the two panes of the slider which can't really be completely sealed and still have a window that opens (at least not with the current design). My guess is that there may be some small openings around the frame. If so, they are easily sealed with silicone such as 3M 3200. There are so many places on the boat above the water line that have sealent around them, it's not unsual for a small gap or two to be found on this or any other new boat. Also, I would imagine that things that were sealed well when the boat was sitting in a static position at the factory can come unsealed after a pounding, twisting adventure. Finally, over time all seals fail (any below the water line should be periodically re-done, any above the water line can generally be repaired as needed). So, new boat or not, keep a few tubes of sealant on board.