Hello mhutson and welcome to Apple Support Communities.
It appears you are having some difficulty with window placement when using an external monitor connected to your MacBook Pro when it comes out of sleep. There are a couple of steps you can take to help isolate the cause of this behavior.
1) Start by doing a safe boot of the Mac. This will clear some cache files, turn off some system extensions and log-in items and give you a good foundation. After doing the safe boot, reboot normally and test.
How to use safe mode on your Mac
2) If the issue persists after a safe boot, set up a new admin user account and boot into that for testing. Doing so helps you to isolate the issue to the system or the user data and ultimately resolve it.
You can find the steps to add a user here:
Set up users, guests, and groups on Mac
Cheers.