That's not a bug; it's simply the "big damage" flag at work. In FS2, any ship bigger than a cruiser has that flag defined in its table entry, which prevents it from being destroyed by conventional fighter weapons; the damage applied by these weapons over the last 10% of hull integrity decreases exponentially, to the point where the ship just can't be destroyed. (Ships with the "supercap" flag, such as the Colossus and Sathanas, have a similar effect applied at 75%.) Weapons with the "huge" flag defined in their table entries ignore the "big damage" effect and cause the last 10% of damage normally; the only player-usable weapons which have this flag are the Stiletto II, Trebuchet, Cyclops, and Helios. The whole system essentially exists to prevent one fighter from taking down a huge capital ship with just a continuous stream of primary fire, such as the trick that everyone used to kill the Hades in the original Silent Threat. I don't think you can equip a weapon with the "huge" flag in "Proving Grounds," and so the Tiamat is very difficult to kill on anything lower than Medium difficulty; even if you stick right next to it, the Aquitaine's beams just don't do enough damage quickly enough in order to take it out.
So yeah, if you put a bunch of Herc II's with a default loadout in-game, they wouldn't be able to take out a Deimos on their own. It may not be the most realistic system ever, but I think it's somewhat more so than letting a Loki with a Subach be able to destroy an Orion.
(Yeah, someone else snuck in, but I extracted table entries to look this stuff up, dammit.

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