"Blue birds are flying over the rainbow."
Translation:Bluaj birdoj flugas super la ĉielarko.
If there is some context in which is clear what you mean, than - yes. If a sentence is grammatically correct and it helps to transfer your thoughts to someone else, then you're using the language properly. There are almost no native speakers who can say "but we do that in a different way, it sounds unnatural, etc".
Esperanto is a Lego-language. You formed a new word (probably because in your mother tongue this concept is expressed in the same way) from the existing building blocks. That's the way how Esperanto works. You have to learn how to form the new words and how to put them to a suitable context rather than to try to imitate somebody's native language.
How do you disambiguate whether you want to express the the flying happens above the rainbow (German: "über dem Regenbogen"), or that they pass through the space above the rainbow (German: "über den Regenbogen"). I would have thought that super+accusative expresses the former, but it was not accepted.
"Bluaj birdoj flugas super la ĉielarko" expresses that the flying happens above the rainbow, where as "Bluaj birdoj flugas super la ĉielarkon" are them passing through the space above the rainbow since the accusative -n in this case shows movement from one place to another. I may be wrong with the second one, though, because "tra", whic means "through", might have to be included somewhere.