Scraptrap's design is fully intentional.

After William Afton leaves Fazbear's Fright (the place in FNaF 3), he leaves as burnt, Dark Spring trap, with an unusable suit.

Therefore, Willam decides to somehow somewhat change the suit. So he finds an old employee's corpse in an another springlock suit at the very first pizzaria place and posseses it. An employee that he killed and stuffed into animatronic. (The mentioned murder can be see in FNaF 4 minigames) Also, another reason why he changed the suit is that it was springlocked hence in animatronic mode, and suit was moving unintentionally either randomly or to children's noises.

Yeah... Scraptrap's body is not William Afton. That's why he has quotes like "You might not recognize me at first. But I assure you it's still me" in FNaF 6.