In general it is a bad practice to use the id property. If you must have some sort of id, use itemId, which will not have any type of global uniqueness constraint and also allow you to use # in your selector.
People generally use ids to make it easy to get a reference to a component, something like: Ext.ComponentQuery.query('#myid');
What you should really be doing is:
Ext.ComponentQuery.query('filters checkboxgroup')
in order to get a reference to your checkboxgroup.
In your case, change the selector in your controller to be 'filters checkboxgroup' and you should be just fine. Note, if you have more than one of these in your application, add more specificity to your selector, for instance, if your filters component is a child of a particular panel:
Ext.ComponentQuery.query('panel1 filters checkboxgroup')