If you find <...> in the box, <...> is the direct object. For 3rd person singular female the direct object form is "la". But here in the sentence there is "le". "Le" is the indirect object form of 3rd person singular female, so that doesn't fit here. It is not 3rd person singular. But it is also the direct object form for 3rd person plural and that matches.
I'm sorry, my answer looks a bit chaotic. Is it helpful anyway?
If you want to say "I find her in the box", the phrase is "[io] la trovo nella scatola".
If you say "le trovo nella scatola", it either means "I find them in the box" (with "them" being feminine, such as "caramelle") or "I find to her in the box" (the latter doesn't make any obvious sense to me by itself).
TL/DR: "le" as an object is either "them" or "to her"/"for her".
This is insightful .. thinking of which use cases apply on a pronoun by pronoun basis. It is certainly helpful in the case of le.
Here is my stab at a (simple, for beginners like me :-) chart for reflexive, direct, and indirect pronouns on a pronoun by pronoun basis.