I think the main reason for the wacky scene at the cetacean institute is that it is a badly written scene. It is there just to fill out her "character" a little bit... and to make up a bogus incident to make us think that the whales are in danger... as if these were the last two whales on earth and that they were marked for death... a very lazy conceit. The "Bob" character has about as much weight drama-wise as "Madeline" in the Plexiglass factory. Just a bit player who is there so that the world seems more real. That's it. It's part of flimsy storytelling... and it's noticeable because apparently the only people working at the Cetacean institute are Gillian, Bob, and the guy who is hosing down the place. (who apparently is doing this all the time, since he is in the background of seemingly all the shots there.) As you can tell, I'm not a big fan of "The Voyage Home"... 
