I'm having an issue with my custom subclass option. It's a subclass for sorcerer and I had the bug happen on the 1st level feature, but it resolved itself. Then it happened again for the 14th level feature. There's supposed to be an option to choose, but it won't register in the builder that it was selected.
Here's the link if anyone can take a look at it and see why it's doing this:

https://www.dndbeyond.com/subclasses/458119-elemental-enabler

I’m not a Mod, so I cannot see your homebrew. However, I have been making a subclass with lots of nested and interrelated options. I posted this for someone else a little bit ago, it may be useful to you. 

https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/67361-subclass-help?comment=4

I followed the instructions, but the option itself is not showing up within the builder. So the player can't even click on the option

Edit: The option is showing up, but the builder itself does not register that I have chosen an option

Usually when that happens it’s because of the settings for the options don’t all match each other. Maybe one is set with a prerequisite that comes at a different level than the other two. Something about one of the options is slightly different than the rest. Once all of that is straightened out and you re-save them all, then re-save the whole feature, re-save the whole subclass, and to actually push through to the character sheet sometimes I even have to delete all of the class levels for the associated class (if it’s an issue with a fighter subclass and the character is multiclass only the fighter levels have to be removed) and then refresh the page, and then add the class levels back and remake the choices and it finally fixed it for me.

This happened with the 1st level feature, but when I remade the feature it worked afterward. I've remade this feature at least 3 times and did the exact same thing I did with the 1st level feature and the builder still won't register that I picked the option

After you remade the feature, did you re-save the whole subclass? If you don’t do that it won’t update. And you might honestly need to delete the class levels from the character and re-add them to get the character sheet to pick up the changes.

I've saved the whole subclass, refreshed the page, deleted levels, and brought them back. Nothing is working

ok, so I went into the creator and followed my first level feature and copied the steps onto my other class feature. IT WORKED! finally

That’s great!! I knew one of them had to be a little off. I’m super glad it worked out for you.

Yeah so, I'm kinda late to this thread but I'm having the same problem. How did you fix the builder itself not registering that I have chosen an option?

After I choose one of them and close the feature tab it simply forgets what I picked, making me choose again.