I'm new to this App so maybe I am missing something.

v4.8.4: Book and chapter only reference in notes, when loaded by tapping reference, loads chapter number 1 of the book with the verse taken from chapter number.
"Gen 3" loads Gen 1:3 (expecting Gen 3:1).
"Ex 5" loads Ex 1:5 (expecting Ex 5:1).

This hasn't changed in a long time, so it's not unique to 4.8.4. We'll be changing this in a future version, but for now, you just need to be more explicit. Use "Gen 3:1" instead of "Gen 3."