Let me guess.....the auto destruct was off line? I don't know how many times they used that poor excuse in Trek but it always made no sense. At the very least, they should have had a bunch of dynamite and lit a fuse like in the old Roadrunner cartoons.
Works for cartoons.
However, in the real world, it's hellishly difficult to scuttle a ship (a thing that floats on water, and at first thought should cease to do so with little effort). Most efforts fail: ships just aren't built so that they would be easy to destroy, not unless a special "self-destruct mechanism" is used. And if that mechanism doesn't work, then you can't self-destruct. Ships don't carry the sort of munitions that could be easily jury-rigged to blow large holes below the waterline, for example.
Really, if there is a need to scuttle a ship
quickly, the preferred option is not to rig explosives or open valves, but run the thing aground (provided there is ground in sight). It will not completely destroy the ship (unless the skipper gets lucky), but at least it will deprive her from the enemy for a few weeks or months; a failure of explosives or valves will not offer even that much of a delay. The 19th century is rife with stories of attempted scuttling by valves or fire and subsequent humiliating capture of key warships, especially in the Americas and the Indian Ocean.
Now, one might argue that a starship
would have one means of self-destruct that is certain to work: the antimatter stores aboard. We have seen our share of accidents in that respect already. But that's like arguing that warships of old had an idiotproof self-destruct system in their munitions magazines or coal bunkers, which often blew up by accident. Not true: it was insanely difficult to deliberately blow up those volatile things, exactly because the accidents did happen, and because engineers then did their damnedest to prevent further accidents.
It just mightn't be technologically viable to build a deliberate weakness into the antimatter containment systems that could then be exploited for self-immolation. Or in other words, the weakness could be built in, but with so many safeguards that if enough wires were cut and pipes bent, it would be impossible to exploit the weakness.
Timo Saloniemi