I can think of 3 things to try here:
Link to the full file. I had this line in a (pretty old) app that worked fine:
app.import(app.bowerDirectory + '/bootstrap/dist/js/bootstrap.js');
Make sure you app.import is inside of the main module.exports declaration in your ember cli build.
You might also try testing it out with a different bower package to see if the problem is bootstrap or your app.
If all else fails (and even if it succeeds), I highly recommend using ember bootstrap instead. It will handle the stylesheets for you and provide some Ember friendly ways to implement bootstrap components. You won't need to do the import anymore. Overall, it's best to avoid mixing libraries that modify the DOM (like plain bootstrap) with ember components. http://www.ember-bootstrap.com