If you use flasks with rubber stoppers and cotton stuffed into the holes of the stoppers, then the foil acts as an additional barrier to keep contaminates from settling onto the cotton and the rim of the flask and possibly working their way into the flask.
Also if you sterilize utensils or other items, you wrap foil around them so that when you remove them from your autoclave/pressure cooker, they stay sterile inside the foil. You can't wrap plastic around them because it might melt.
Hope that answers your question.
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