I checked the file but I can’t find a bug. I tested your course in moodle, but it’s tracking the score correctly. Question 3 seems to be correct, I can’t see anything that may be different to the other questions. The Exit-Button should not cause a problem neither, if the window is closed the test is not processed so there should be no score.
All variables in your test are “retained between sessions”. If a learner answers questions 1 and 2 correctly, closes the window, reopens the course, is directed to question 3 by the bookmark, answers “only” Question 3 correctly, clicks “Done” the test result should 100% as the answers to 1 and 2 are retained.
What exactly does the LMS display as a score for these users? 100% or 33%? All relevant values in the course are correctly set to 80. Which LMS is it? Is there a setting that may overwrite the mastery_score provided by the course?