Because prior to the ability to actively see cells and then further experiments in the 1600s and 1700s to most people it would seem like a leap in logic that small creatures are causing food to smell rotten. Things just became rotten over time because that was in their nature to.
Also, the belief that bad smells caused things to rot was strong. If you lived a millennium ago it would be easy to believe that the smell of a rotting piece caused another piece of food to go bad because it also started to smell. And if you ate a foul smelling piece of food you might also start smelling bad.
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