Firstly, don't worry - you should never need to go over budget for a Prolific study. 

If you check in 'View submissions' you should have only the total number of submissions you requested awaiting payments. 

Possible reasons for extra submission in your study data include: submissions that were started by 'Timed-out' or were 'returned' (see http://help.prolific.ac/managing-submission/missing-prolific-submission-in-awaiting-review). Or duplicate submissions from a single Prolific participant (see http://help.prolific.ac/general/researcher-faqs/some-participants-have-taken-my-study-multiple-times-why-is-that). 

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