This clone demonstrates a problem I have when having prototype.js loaded in the same page of ember. Ember's initialization flow is distrupted and the internal Ember objects (Application, View etc) are undefined.

Uncaught TypeError: Object #<Object> has no method 'each'
collect prototype.js:864
initMixin ember-0.9.5.js:5927
Mixin.creat eember-0.9.5.js:6175
get ember-0.9.5.js:6394
(anonymous function)

With ember.min:

Enumerable.collect() at prototype.js:485
n() at ember-0.9.5.min.js:10
b.create() at ember-0.9.5.min.js:10
(anonymous function)() at ember-0.9.5.min.js:10
(anonymous function)() at ember-0.9.5.min.js:10