I've found the bugs. Green means lines to be added. Red means lines to be removed.
main.py
Wrong indentation. This is not a compilation problem, but it prevents your program to run correctly (to use the right logic).
line 21: run_test(questions)
line 21:run_test(questions)
Question.py
You misspelt the __init__ function.
line 2: def __init_(self, prompt, answer):
line 2: def __init__(self, prompt, answer):