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Last, there was also an explosion from the inside that is separate from the missile probably caused by its shock wave.

The article says that it might be from the missile.

Another possible explanation could be the detonation of a dual 'BROACH' warhead, like that carried by the Storm Shadow and/or SCALP-EG cruise missiles that are widely reported to have been used in the attack.

https://en.wikipedia.org/wiki/BROACH_warhead

The Bomb Royal Ordnance Augmented Charge (BROACH) is a multi-stage warhead developed by BAE Systems Global Combat Systems Munitions, Thales Missile Electronics and QinetiQ.[1][2]

Development of BROACH began in 1991 when Team BROACH consisted of British Aerospace Royal Ordnance Defence, Thomson-Thorn Missile Electronics and the Defence Evaluation and Research Agency (DERA). The two stage warhead is made up from an initial shaped charge, which cuts a passage through armour, concrete, earth, etc., allowing a larger following warhead to penetrate inside the target. The weapon is designed to allow a cruise missile to achieve the degree of hard-target penetration formerly only possible by the use of laser-guided gravity bombs.

If that's what happened here, I have to say that while I don't think that it was designed for this as such -- I mean, a submarine isn't really armored per se -- it does seem to have caused quite a bit of damage.