I may be misreading you, but it sounds like you've either not issued one of the proper shutdown commands or have unknowingly changed your root password.
There are a handful of ways to shut down the pi, my favourite method is the following:
This will also work, and is perhaps easier to remember:
You will need to enter your "raspberry" password for both commands, because they require sudo elevation.
If the "raspberry" password isn't working, then it's possible you might have changed your root password. The easiest way out of this I feel would be to backup your existing work and reset the Pi back to it's original state. If you're running NOOBs, then this is a simple case of holding down SHIFT on boot and following the instructions.