I have an 11th level bard and it only thinks I have 2 spells from magical secrets.  It should be 4.

https://imgur.com/a/eC73OFy

The 6th level Lore Bard Magical secrets do not count as known spells. They're extras to the amounts of spells a Bard learns.

All other Magical Secrets for the Bard are "known" spells - they are included in the maximum of known spells. This means as an 11th level Lore Bard you should know 17 spells, maximum. 13 will be from normal ones you select as you level plus 2 from the 10th level main class Magical Secrets (the "2 spells included from class features" you see in the image you linked) to make 15, plus 2 more from the 6th Level special Magical Secrets from the College of Lore feature.

Here's the 10th level main Bard Magical Secrets, with some bold part highlighted:

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.

Now see the 6th Level Lore Bard Magical Secrets:

Additional Magical Secrets

At 6th level, you learn two spells of your choice from any class. 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 but don’t count against the number of bard spells you know.

I hope this highlights the issue. 

From the Class Spells tab, you would have 13 picked there. On the Class tab at 10th level you'll have selected 2 there, making the 15 normal bard spells you know. At 6th level you'd have selected two there, which will not count towards your known spells.

I hope this explains things.

At 11th Level you only have 2 Magical Secret spells. You learn another 2 at 14th and again at 18th.

Quote from Ariiss42 >>

At 11th Level you only have 2 Magical Secret spells. You learn another 2 at 14th and again at 18th.

Lore bards get 2 extra at 6th level, and the OP mistakenly thought they should be considered in the message about "2 spells from class features", when they don't.