A student submits a quiz on time and earns a score. Student accidentally starts a new attempt, never finishes it. Canvas does student a favor and automatically submits the second attempt for student when availability window closes. Now that there is one "late" submission, best (on time) score is penalized with late deduction. This has always (seven plus years) been a problem. I see comment threads here going back to 2019 addressing the issue. They are marked as "resolved" but link to a product release that allows instructor to manually remove late flags.
Apply late flags only to late submissions. Then decide which score to keep as highest after the late penalty has been applied correctly.
