When working with ember-cli and things seem to get messed up and you cannot figure out for the life of you what's wrong you can always resort to nuking it all and refreshing the environment.

This often helps me alot, and although I do not know for sure the exact details behind the reason it fixes things, I don't care as long as it works.

In my ~/.bash_aliases I've added the following aliases, a "regular" fix nom and a "nuke-it-all-and start-over-again" fix nomallas follows:

alias nom='rm -rf node_modules && npm cache clear && npm install'
alias nomall='rm -rf node_modules && npm cache clear && npm install && rm -rf bower_modules && bower cache clean && bower install'
...
alias realias='$EDITOR ~/.bash_aliases; source ~/.bash_aliases'

Just run realias to make the required changes and you're all set.