I've had the "We're taking damage sir!" yelled at me over and over at loads even when I had no hull % damage or any red damage. However, I *had* had damage and repaired it recently before the save.
All kinds of crazy things can happen when you first load a save. I've had "Torpedo missed sir!" repeated over and over at load even when I hadn't fired any torpedoes in a good long while.
I say don't worry about it, just pay attention to whatever the damage screen displays. Maybe our crew went without O2 too long or something.