Just wanted to point out that the premise of your question is slightly off.

The tone of your question implies that a person in power (currently ruling) would kill one of their heirs. This was unnecessary, given that they could change the heir if they wanted or could adjust the rules regarding succession. After all, the ruler is ruling, so unless they were just puppet rulers, they had power to adjust things to their desires. For the most part, something like "King Bob killed his eldest son just because he wants his second son to rule" wasn't really a thing. He could figure out a way to make it so without killing people.

One quite recent example of this is currently reigning Salman of Saudi Arabia. Upon rising to the throne, the Crown Prince title (heir to Saudi Arabia's throne) was transferred to Salman's half brother Muqrin. Soon thereafter, Salman transfered the title to one of his nephews, Muhammad. After Muhammad was arrested and charged with treason, the title was then transfered to Salman's son Mohammad.

Instead, the deaths of heirs for heritage-related reasons (like adjusting who would inherit the throne) were mostly done by those who weren't ruling. People who couldn't change the rules and appoint the ruler they wanted. See the above list posted by someone else for a ton of instances for when, why, and how these deaths happened.