How did you create the installer?
If you downloaded macOS Sierra, through the Mac App Store, the official way to get Apple Mac OS versions, then in your Applications folder you will then have the Install macOS Sierra app. There are a few ways to make the USB, I recommend Terminal, but here is a
link with the different options to create the USB.
It sounds like you may need to erase you current OS drive to sort things out. Of course, make sure you have a good backup of your Mac OS drive and your Boot Camp drive.
Fusion drives are funny especially with Boot Camp. What I would do, is;
backup Boot Camp
make the drive one partition
Next, I would back up the new single Mac partition
then attempt an erase and install.