What in the world is happening on Handbrake on my Mac?
Did you remove the VLC player ?

Because HandBrake no longer includes the libraries needed to decrypt commercial DVDs, you’ll also need to install the VLC media player. 

To get the 64-bit benefits from HandBrake, you’ll need to have a 64-bit version of VLC as well. 

The standard download is a Universal Binary and contains both 32- and 64-bit code for Intel Macs—if you want to save some disk space, you can download the VLC specific version here.