Windows resize on primary monitor when I wake up the computer. Dual monitor setup
So for anyone that might have this issue, in my case it was as simple as rebooting into safe mode. 

I held down the shift key after the startup sound, released it when I saw the apple icon. After it successfully rebooted into safe mode I simply did a normal restart. I suppose this cleared out system caches and the windows stay put now after I wake up the displays. 

*One weird issue when booting into safe mode that might help others as well. For some reason I had an issue with only seeing a cursor and a black screen. I assumed for some reason the login window just didn't display properly and I hit Escape and typed in my password as usual. I then noticed a spinning beachball and it logged in.