Hyphens are highlighted as substituted glyphs

I often fail to fully understand what the OP is asking. 

Is it even possible for InDesign to substitute the font?

Hey Stan,

Why not simply turn off the radio button for Substituted Glyphs? All these onscreen color hintings are hyperactive over-doers and largely unnecessary once you have made a well-balanced Paragraph Style.

In a paragraph style for body copy, be sure to add these settings for a well-balanced style:

Hyphenation: 9, 3, 4, 1, off, off, off

Justification: 80/100/120 and also -5/0/5% and also 95/100/105%

Try it. You'll like it. And a well-made style largely obviates many typesetting problems as a result of its flexibility.

And SC: since InDesign makes the decision to inject these hyphens according to its spell check dictionary, it is a case of substituting formerly nothing with a hyphen that you had not keyboarded; hence a substitution made by the application.

A violation is InDesign saying: "I cannot typeset this line according to the rigid rules you have applied to the paragraph. I'm going to do what I want to do instead. I will signal to you that I have disobeyed you by this on-monitor color highlight."

@Stan Buls

Shouldn't they be pink'ish - instead of yellow? 

Can you share a sample document?