Near the end, all but Tuvok and Janeway have used the escape pods to abandon the ship. When we see the external views of the ship, the escape pods are still in place.
B'Elanna reminisces that she spent weeks with the Dreadnought programming her the first time to target Cardassians, but this does not square with her earlier story that she sneakily sent the weapon on a new mission without asking Chakotay. Under what conditions would Chakotay not notice either that B'Elanna is off his ship for an extended period working on the probe, or think she was doing something on the probe other than reprogramming it?
Earlier versions of Star Trek set the precedent that it took two officers to activate the self-destruct sequence (one to initiate it and a second to concur). In this one Captain Janeway activates it on her own authority.