What do Japanese waiters/waitresses often say when they bring you the bill at a restaurant? I responded with 別々にお願いします and my waitress at Kappa Sushi was confused.

レストランでお勘定を持って来る時、ウェイターは何をよく言いますか？

質問を翻訳

I'm not sure, but maybe something like this?
ありがとうございます。お会計はこちらになります。

I think you should say the object in your sentence to avoid the confusion.
会計を別々にお願いできますか？
And it would be considerate of you to ask that before the bill is brought to your table because 別会計 needs some calculations.

Oh, you don't say that when you are alone, do you? If you do, that must be very confusing because you don't have no one to divide the payment.