Whenever I try to add extra spells via the Magical Secrets feature, the spell selection will show a red exclamation mark, telling me that I'm over the spell limit and need to delete some spells.  But then I also see an asterisk message that says "2 spells included from class features."  Why are spells gained from a feature other than Spellcasting count against your Known Spells?  

Here is my character sheet so you can gain greater insight into my issue:  https://www.dndbeyond.com/characters/73270420 

Magical secrets spells are supposed to count against the number of spells known, that’s why bards get additional spells known at those levels.

Magical Secrets

By 10th level, you have plundered magical knowledge from a wide spectrum of disciplines. Choose two spells from any classes, including this one. A spell you choose must be of a level you can cast, as shown on the Bard table, or a cantrip.

The chosen spells count as bard spells for you and are included in the number in the Spells Known column of the Bard table.

You learn two additional spells from any classes at 14th level and again at 18th level.

Quote from IamSposta >>

Magical secrets spells are supposed to count against the number of spells known, that’s why bards get additional spells known at those levels.

Ok.  So the main advantage of Magical Secrets is learning spells outside of the bard spell list.  Makes sense.  

If I'm understanding correctly, Magical Secrets doesn't give you more spells than normal, it justs gives you more options.  

If you want some extra confusion, the Lore Bard's "Additional Magical Secrets" feature spells do not count against your number of Spells Known.