I am Ukrainian. "цибуля" could (should) be both singular and plural. It same as "metro" or "sugar". Here is mistake about keeping only plural.
How do you say, "Yes, with vareniki?" Is it "Так, з варениками?"
Why is there a singular plural switch?
In the first sentence noun "tsybulya" is the subject, whereas in the second sentence "tsybulya" is a direct object (it takes accusative case).