In the Druid subclasses with extended spell lists, they show up at 3rd level, but the ones without can't be complete without a third level ability.

Well, you don't need an expanded spell list. I sometimes do something small, like a cantrip or similar power. But it's because the base is circle of land, which has a 3rd level ability. It's weird. 

This is the case for all sub-classes, as the base class must specify a number of levels at which sub-classes are required to have traits. You can add additional stuff at other levels, but you must have at least one trait for each required level.

You can however add anything you want, it could even just be a note which you set as hidden in the character builder and character sheet.

I make a 3rd level class feature. I call it ".." with a description of "." I set it's display order 9th and check hide in character builder and hide in character sheet. I don't think the hide in character builder option works though.

It shouldn't do, if you didn't select the option right away though then it might take time to update (a lot of homebrew content takes around 20 minutes to be updated from the moment you save the sub-class/feat/whatever itself).

You should put something in though as even if hidden in the builder and sheet it will still appear on the sub-class page viewed in the homebrew list or going to view full details, for example you might put a note about the sub-class, how it can be used, the types of characters it's suited for, how you might become that sub-class or such.

Or you can use it to add a minor bonus, like a cantrip as BramblefootDruid suggests, or a bonus proficiency or anything really.

I agree hide in builder should work, but I have not found that it does. Due to this some explanation blurb would be more useful on the character builder. Using my method leaves the subclass details page with little useless information.

For example: the level 14 subclass feature and the following ".." level 3 subclass feature: