https://jsfiddle.net/2j5gx35j/11/

When working with Select2 , if dropdown list of select2 cover pretty-checkbox, after click select2 item, will also cause pretty-checkbox seleted.

May this two css rules is the reason:

z-index: 99999999;: https://github.com/lokesh-coder/pretty-checkbox/blob/master/src/pretty.css#L63

opacity: 0;: https://github.com/lokesh-coder/pretty-checkbox/blob/master/src/pretty.css#L71