I think it should look like 

var base = Class.create({
    iterations: 0,
    initialize: function(item) {
        this.iterations++;
        //this.collection = [];
        this.collection.push(item);
        console.log('Iterations: %s, Number items in Collection: %s', 
this.iterations, this.collection.size());
    }
});
var foo = Class.create(base, {
  collection: []
});
var bar = Class.create(base, {
  collection: []
});


Collection in your sample was actually base.prototype.collection and was 
shared by all child classes and instances.

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