This is a problem with subject-verb agreement. You want 'does' and 'classifies' to agree with each other. We drop the s at the end of verbs when using 'does.' So the correct question would be "Why does the light blue line classify so bad against the other?" Does and classify agree with each other.
You were trying to ask a present tense question and knew that you needed to use 'does' in this sentence. When the subject is he, she, or it use 'does' and drop 's' at the end of the verb.
We use 'do' when the subject is I, we, you, or they. An example of this would be "Do they walk to school?" or "Do you write books?"
An example of 'does' in a question would be "Does she use iTalki?" or "Does he classify notes?"
I'm confused on what you're asking. To classify means to put something in categories. Is the line classified against another line?
I get the sense you want to use the word contrast, which is often used when describing a striking difference in color.
"Why does the light blue line contrast badly against the other?"