Complex Program Freezes and Breaks

That sounds to me like the browser's memory is getting overloaded. Are adding a ton of elements in the draw() function? As the game progresses and you keep adding elements without clearing old ones, the memory can fill up and cause the program to freeze.

Also, watch for infinite loops, of course.

To really be certain it's not just a Khan Academy-specific bug, you could try running it in a different environment, like for example locally on a dev server. Is this a ProcessingJS game? If so, in order to run locally, you'd need to run your code in an HTML webpage file and import the ProcessingJS library so your game code can run outside of KA's playground. Here's a guide on how to do that:
https://www.khanacademy.org/computing/computer-programming/programming-games-visualizations/advanced-development-tools/a/using-processingjs-outside-khan-academy

Good luck!