Bots have become a problem. A user has written a script for generating thousands of accounts and getting them to 5,000 energy points, then voting up whatever programs they want. They "tested" it on my MineKhan program first, then removed the votes for it a couple days later. I track daily votes on all programs for a graph, and this is what it looked like.
The user also made this and has talked about plans to slowly add votes to their own programs to avoid detection.
Solving a captcha in a popup window the first time an account votes for a program would be the least invasive solution to this problem. A captcha on account creation would be more typical, but would affect all areas of Khan Academy.