[Solved] subtraction not working in java program (missing something)

Its very simple you are not calculating applesToOrder and orangesToOrder again after user input so they are taking there previous values of 0, just put these lines just above your last JOptionPane statement and see the magic.

 applesToOrder = applesTheyNeed - applesTheyHave;
 orangesToOrder = orangesTheyNeed - orangesTheyHave;