"Where are the boy's pants?"
Translation:Wo ist die Hose des Jungen?
Yes, normally masculine and neuter nouns add an "-(e)s" in the genitive singular. You're also right that "der Junge" is an exception. It's a so-called "weak noun" (n-declension). For more information on weak nouns, see: http://www.vistawide.com/german/grammar/german_nouns03.htm
Other weak nouns frequently used on Duolingo are "der Elefant" (the elephant) and "der Bär" (the bear).
The "von + dative" construction is a colloquial alternative to the genitive and perfectly acceptable. However, you used the plural (the boys') instead of the singular (the boy's):
die Hosen von den Jungen = the boys' (pl.) pants
die Hose von dem (or: vom) Jungen = the boy's (sgl.) pants
"Junge" (boy) belongs to a special group of nouns, the so-called weak masculine nouns or n-declension. These nouns add an -(e)n in all cases apart from the nominative singular. So you say "Junge" in the nominative singular (e.g. Der Junge ist intelligent = The boy is intelligent), but "Jungen" in all other cases in the singular and in the entire plural. You can still distinguish the singular and the plural by the articles, though:
Wo sind die Hosen des Jungen? = genitive singular. Where are the boy's pants?
Wo sind die Hosen der Jungen? = genitive plural. Where are the boys' pants?
For more information on weak nouns, see:
Two months on, and they're still not accepting die Hose, even though the English pants can very well be translated to the German singular and there is absolutely no context to let us know that the English is actually referring to multiple pairs of pants (which can only be die Hosen, plural).