It is APE's fault. It's their software that has (mostly) caused this.
However, the blame may not lie with APE.
Do you own a Logitech product, like a mouse or keyboard? Their drivers install with APE's software (why they ever decided to do this is far beyond me). But, it never tells anyone in clear language that it's using this software, so many don't realise it's been installed (and all just for a mouse driver!).
If it is that, then it's entirely Logitech's fault. APE is software that modifies Mac OS X, and as such can cause problems when upgrading, which is beyond what Apple can check for (since you made the modification).
1) I hope you have a good backup.
If you're comfortable with the terminal and know that your system is going blue due to APE (not all the blue screens have been caused by this, but most have), then I'd use their 2nd recommendation.
Else, try their first recommendation.
Good luck!