"There was a thunderstorm all night."
Translation:Estis fulmotondro la tutan nokton.
why does the hint show fulmotondron when it is WRONG and why is tutan nokton in accusative after estis
Tutan nokton is an accusative of time, which is totally independent from the verb. It just replaces an adverbial (tutnokte) or prepositional expression (dum la tuta nokto). Esti is not used as a linking verb here, neither in English nor in Esperanto. Therefore there is only one nominative. Storm is not linked with night.
For nouns, the hints are not limited to the correct case for nouns. It it just shows that fulmotondron is one of the correct translations for thunderstorm.