Could you please let us know which extra’s are you talking about? Are you using any plugin for that? If yes, then it would be great if you can share a plugin copy with us so that we can check once with that.
Do let us know so that we can assist you in a better way.
I have the same problem. I have the Woocommerce Food install. It give me the option to put add-on in my products, like a pizza with 4 or 5 topping.
But when I print the order, only appears the first topping select.
With customer choose 3 topping, only appears one topping in print.