Copy and Paste: When you are running dual screens, you can not copy from one screen to another.  For example, if you have some text in Word in your screen on the right and need to paste it to Outlook in your screen on the left, it will not paste.  You have to bring both applications to the same screen before you can copy and paste successfully.

Keyboard Shortcuts: Most windows shortcuts do not pass from your keyboard on the Chromebook to your virtual machine. You'll need to work with the mouse.  For some power-users this is a difficult transition.

Chrome Apps: The Office365 applications that you can download for your Chromebook in the Google Play Store are actually Android apps designed originally for phones and tablets and as such, behave more like phone apps than laptop apps.  They have different views and in some cases reduced functionality. One solution to this at least with Office apps is to use www.office.com. After logging in, the Office apps in your browser behave much more like the more traditional Windows applications.