Filter using two taxonomy vocabulary
If you have to use two taxonomy vocabulary instead one, you can do the following.


On the "color" vocabulary add entity reference to the "containers" vocabulary and for each color term set avaiable containers for it.
Using Drupal.settings you give information about relations between terms (as an assocated array, for example) to browser so that it would use information in JavaScript.
Add JQuery script, which intercepts a selection of a color term and delete redundant terms in the select box for containers. That is, for example, you have selected a color Green and JQuery script has immediately removed all elements from the select box for contaners, except "B" and "C".


You can add the JQuery script and send data to Drupal.setting using hook_form_alter for the node insert/edit form. 

Of course, I'm not guarantee that this way is the rightest one, but if I were you I would try so at the beginning.