I saw two problems that can be eliminated very easily.

1. Based on bower.json specification please see the highlighted text below:
   Only one file per filetype.
   Do not include minified files.
   "main": [
   "dist/select2-bootstrap.css",
   "dist/select2-bootstrap.min.css"
   ],
   So these two rules are ignored in this case, but the best solution would be declaration of scss file as entry-point in order to be consistent with Select2 core. This is very important when you use with nodejs something like main-bower-files or wiredep .
2. Also it is very important to add !default flag to all variables under select2-bootstrap.scss file.