I have multiple Custom Post Types, named 'Companion', 'Digital', etc. I also have custom taxonomies named issueDigital, issueCompanion, etc.. I separated them out in the beginning, rather than using ONE issue taxonomy and applying them to all CPTs, simply because the data was shared between all CPTs. Issues from Digital would show up under Companion, and so on.

My quick fix was to separate them out, but now that I am nearing the end of the project I want to revisit this problem and create one custom taxonomy which is applied to multiple CPTs but doesn't share data with each other. I am most grateful for any input.

I've only found this which isn't ideal because you have to remember the following:

One simple way to stop the records from being shared is to make the admin user define a unique slug for each term that shares a common name with another taxonomical term, ie: ‘Red’, ‘red’ in taxonomy ‘A’ and ‘Red’, ‘red-2’ in taxonomy ‘B’, etc. Obviously the drawback is that you have to remember to do this, have to remember how many different ‘red’ terms there are, all easy stuff to forget until it’s too late.