As in on a league table? A method of separating two teams who are tied on equal points, they use goal difference. Goal difference is goal scored minus goals conceded, the teams at the top of the table usually have high positive goal differences and teams at the bottom usually have high negative goal differences.
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You cannot get negative points in football. Where I think you have got confused is goal difference, the amount of goals conceded is deducted from the amount of goals scored by a team to calculate their goal difference.