5

enter image description here

I understand that mistmached furigana can be used to show another layer, but I can't figure out how to interpret this.

I guess it's highlighting the word メイン. Like the hamburger is the main thing she took?

5

メイン means "main dish" in this context.
From the Wikipedia entry on main course:

The main dish is usually the heaviest, heartiest, and most complex or substantial dish in a meal.

So it goes without saying it is also the thing most people would look forward to enjoying. In the scene in question, メイン doesn't mean the main thing she took, but it is saying she took the main part of the other girl's meal. Note that it doesn't have to be a full course for this word to be used.

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