Can creatine (or whey protein) use during an intense weight training regimen cause a hormonal imbalance? if so, can this lead to acne breakout?

It's not protein: The stress of a excessive excercise can play a trick on your brain so that you don't stimulate your ovaries. Then again if having periods your ovarian hormones are ok. People pin irritability on ovarian hormones when they are not the primary issues. If you are not sleeping well at night, anxiety may be creating issues that feel "hormonal".

Not the issue: If you are using the common supplements that promise to increase "testosterone" naturally, these will lead to acne. They do not increase testosterone, but they can increase the pre-hormone materials that cause acne.