Hello, love the site! I do have a problem however that I have not yet seen in forums.

Problem: 

I homebrewed subclasses that (in theory) are flexible and replace typical subclass features with the option to at times choose multiple feats.

(Link to example Ranger: https://www.dndbeyond.com/classes/587773-custom-class-ranger/subclass/587773/edit )

However when in Character Builder, if I choose a feat through 1 of the options available, this duplicates the choice in the other "Choose a feat" options instead of allowing me to make separate choices.

Fixes?

I've had the same issue, I've had to add the individual "Choose a Feat" modifier in separate class features.