Also, maybe the destruct method was corrupted by the damaged nature of the Enterprise.
Between the limited repairs left from TWOK and the hit from the Bird of Prey, the damage may have affected the destruct system. What we saw in TSFS may be a self-destruct mishap, where certain scuttling charges didn't go off as designed or detonated prematurely out of sequence or whatever else you can think of. A self-destruct that didn't go as designed.
Plus Voyager and Nemesis showed that its possible for battles damage to completely disable the self destruct, so it being partially disabled isn't that much of a stretch.