No problem. 
As for the culprit...
If the disk is empty, you can wipe the whole drive in GParted by going to Device → Create Partition Table. This clears everything -- partitions and the boot loader, like a fresh drive.
Otherwise, if you don't want to wipe that disk, one trick is to install GRUB's bootloader in place of the Windows remains... that'll prevent this from happening in future: 
sudo grub-install /dev/sdb
For making the second drive a dedicated data drive...
The easiest method would have been to use the "Something else" option when installing to make the second drive the /home mount point. Personal files are stored there.
Now it's after installation, we'd have to do this manually. There's a few ways to do this, and may involve editing /etc/fstab. I do it a bit differently: