In

Perhaps it is some conceptual, developmental milestone that she hasn't reached yet. Perhaps it is something about the pronunciation that makes one easier to say than the other. Maybe she is just picking up Latin. Whatever it is, Brynna uses "in" to mean both in and on.

Usage 1:
The rocks are in the (partially disassembled) Zebra.

Usage 2:
The rocks are back in the box.

There's probably an "into" usage in there as well, but it is difficult to discern. She is only just now putting two words together into a sentence ('ight on. 'ight ow."), so we can't yet tell what declension she's using with her nouns.