By default, the Control key shouldn't be getting confused in VirtualBox unless you specifically set it otherwise; both left and right Control keys should behave correctly when the VM is in context.
However, it does sound like you might have hit the LeftCommand-F combination which may be configured in VirtualBox as "tell VM to go full screen". I believe typically the left Command is the "host key" and operates as it would on OSX for things like hiding windows, quitting applications, etc. The Command key on the right of the keyboard is probably being passed down as the Alt or Windows key to the VM.
All that being said, it sounds like you're hitting Command instead of Control and you're using the left instead of the right. These settings can be changed in the settings / preferences of VirtualBox if you want to modify it.