Over the years, we know Transformers have been mixed up. That is, the character of Sunstreaker (then called Spin-out) was meant to be a yellow Sideswipe mould, while Sideswipe was supposed to be a red Sunstreaker mould. But there are others I've always been suspicious of.
Windsweeper and Dogfight seem like their parents may have mixed them up at the hospital. Windsweeper has chrome, fast-deploying missiles like the Autobots Backstreet and Override, while Dogfight's are slow and matte like Ruckus and Crankcase. Also I've always thought Windsweeper's colours and altmode were more 'Autobotty' than Dogfight's, who in turn would fit in better (colour-wise) with the Triggercons.
Longtooth and Stranglehold - totally mixed up in their cribs. Switch them around and the Decepticon Pretender Juniors would be led by a skull-faced monster and have an octopus and walrus with skull belt buckles as his cronies. The Autobot Pretender Juniors in turn would all be human, as is consistent with every single other bipedal Autobot Pretender. Longtooth was totally meant to be a Decepticon.
Anyone else? It doesn't have to be switched moulds, it can be names that seem mixed up too like... perhaps Battletrap and Flywheels. (Their names were the opposite to usual in their first Japanese cartoon appearance, which is kind of logical since the tank/fighter jet is more suited for battle and the ute actually has wheels. See the video here.)