Translation:Birds fly in the sky.
Yes, it should be. Without the addition of a counter, a quantifier, or a demonstrative adjective [e.g., 一羽(one+bird counter), たくさん(many), あの(that~)], there is often no way of determining whether an object is intended to be singular or plural. Without context,「とりはそらをとびます」is entirely open to interpretation. Yes, it could be a general statement, "Birds fly in the sky." But it could also be "A bird flies in the sky" (as opposed to "A fish swims in the sea"). I would say that I prefer the plural interpretation in this case. However, had the verb been conjugated to the present progressive (とんでいます), I would definitely prefer the singular interpretation (although the plural is equally plausible). English is the biggest obstacle to learning Japanese.
The audio currently seems to be off; そら is being pronounced like そりゃ. I've reported it.
Just to complement my own answer: In this case, the particle は is making the subject "bird" in general. It's like saying about birds, they fly through the sky. If you want to be specific, you can add この/その/あの to convey the idea one bird in specific can fly (but some others don't). If you want to express the idea about numbers, you can use the sentences shown in this lesson.
Japanese relies heavily on context. You may think it is a bird or birds, depending on what was stated before. Duo only gives one statement at once, so it is kinda impossible to guess, but in daily talk, things get easier.
The correct translation was listed as "The bird flies in the sky," but my entry of "the bird is flying in the sky" was marked incorrect. Can someone with a stronger background in grammar than mine explain the difference?
the usage of を here is very unclear because the particle that indicates moving while doing something is で
To quote EquanimousLingo's comment: "を is used when the verb is one of movement, or moving along a path or medium."
That's because there shouldn't be. It's a general statement about birds, not about a specific bird.
It can be about a specific bird. Japanese doesn't grammatically differentiate between definite and indefinite nouns unless through words like "kono/sono/ano" ("this/that").