Because there are 45 minutes in each half with an addition time added at the end of each 45 minute half for any time that they stopped the game during that half for an injury, an altercation, to clean something up that a fan threw on the field, etc...So they may add an additional 3 or 4 minutes to a half and its easier to count up to 49 minutes for example, rather than minus 4 minutes.
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the clock counts down to show how much time is remaining in the game, it doesn't really matter which way the clock counts, but to me it does make more sense to know how much time is left in the game rather than how much time has elapsed in the game.
Because its the natural progression of time from zero to forty minutes. The referee will stop the time count when they feel that a situation will take out valuable playing time so that 80 minute playing time is used.
There is a clock wind up in soccer so as to remind the fans of the action that have taken place during the entire season.