I actually saw a reasonable explanation for this once: battleshort[1].
That is, sometimes equipment has its fuses bypassed because under battle conditions it is better to have the equipment working in a dangerous state, than not working at all.
So when the ship goes to red alert all the major systems are automatically put in battleshort mode. So a couple of ensigns die rather then the weapons stop working because a fuse blew.
[1]: https://en.m.wikipedia.org/wiki/Battleshort