To my knowledge there is no third party software that makes you just unable to be hit by something, only dodge it with a script, so if you say it go in their hitbox then it was not a script either. The problem is most likely hit boxes, but not that they are broken, but probably more that you do not know where they are. The hit box of a champion is almost a circle around the feet, legs and lower back of a champ to account for the angle of the third person view the player has so if something is "always missing" typically aiming slightly lower will help. NOTE: this is not to say some hit boxes are not bugged and are in the process of trying to be fixed. There are also items that could negate your damage all together (i.e. Maw passive can pop and block the damage, Banshee/Edge of Night Shield negate a spell and then there are Spell shields like Sivir and Nocturn who can negate one spell that its or Morgana that blocks magic damage and cc as long as it is on).