I sometimes have a contamination in the culture bottles (usually fungus). However, when I examine all the used media I do not find any contamination in these media.

Answer

Often fungus contamination does not affect the media color ( if phenol red is present) or clarity.. If you are using original media bottles and not transferring the media I would worry about how the contamination is occurring. If you transfer your media for some reason, to a glass bottle I would heat treat them. Maybe use an antimycotic?