I was recently diagnosed as hypo and now take 50mg of levothyroxine and have intense headaches, hot flashes, and flushed cheeks- why?

Call md. You need to be reevaluated for the amount of levothyroxine. That sounds like it is way to much so call asap.
Check your levels ! It may be too much of a dose. I will verify the accuracy of diagnosis with an endocrinologist and consider adjusting (lowering) dose if indeed what you are describing is due to high thyroid levels. Always verify dose on your prescription bottle !