Yes
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The bonus action has two criteria for triggering:

 - You take the Attack action
 - You make an attack with a light melee weapon

If you have multiple attacks in a single Attack action because of Extra Attack, you only need to consider a single one of the individual attacks you make when triggering the two-weapon-fighting bonus action, not the entire Attack action and all attacks you made as part of it.

So if you are fighting with a shortsword and a hand axe, and you make one attack with each as part of your Attack action:

- You took the Attack action and made an attack with your shortsword, so you can use a two-weapon-fighting bonus action to make an attack with the handaxe
- You took the Attack action and made an attack with your handaxe, so you can use a two-weapon-fighting bonus action to make an attack with the shortsword