In fighting game lingo, a disjointed hit box is when the hit box of an attack (the part that can harm your opponent) is separate from the hurt box of the attack (the part where your opponent can harm you). This is a huge advantage in terms of spacing, because you can attack from certain ranges without fear of counterattack.
For example, the swordsmen in Smash (Marth, Lucy, Ike, Metaknight, Links) all have disjointed boxes on their sword attacks--the sword can hit you, but you can't hit their sword. So you'll notice that skilled swordie players will keep their distance from you and throw out attacks from a range where, for example, Mario's fTilt would get his leg hit by Marth's fTilt. Technically, you could say all projectiles count as disjointed boxes, as well, but usually people won't refer to them that way. It's good to fiddle with your move list and look for these disjointed boxes, since they tend to be good things to trade with during the neutral game. A few examples include: Mario f.Smash (the fireball), MegaMan f.Air/b.Air (the blades), Pikachu f.Smash (the thunder ball), Charizard d.Special (the rock)