These are the ones that always get mentioned, but over the game's whole history there are too many great bugs to name. One infamous one that I recall from the early days had to do with the lethality of carp. You see, Dwarf Fortress features character progression. Your dwarves have not just skills (armorsmith, record keeper, surgeon, conversationalist, cheese maker, etc.), but also basic stats: strength, agility, toughness. The way that you increase your stats is by exercising your skills. And of course every entity in the world is simulated in the same way, because why wouldn't it be? So what made carp so dangerous? Well, every game tick every carp on the map had to make a swim check to stay afloat... and swimming is a skill! So shortly after loading a map for the first time, your carp will have leveled up into legendarily tough, fast, and strong terrors. And because world generation often populates maps with tiny disconnected pools, and then places carp in those pools, the carp AI considered itself perpetually cornered, making them extremely aggressive! Thus the result is that any dwarf walking adjacent to a pool (which they often will of their own accord, to drink or (ironically) fish) will find themselves being bitten by a hulking super-carp and wrestled beneath the surface of the water to drown.

So what do you do against this existential threat? Well, you wait for the first winter, at which point the map freezes over and all the carp asphyxiate. Fun!