This shows one of the very good reasons to not program any tones for a scanner unless there are specific reasons to do so. Programming a tone into your scanner will restrict what you hear (you'll only get transmissions that match your settings) and increase the time the scanner takes to start sending the audio to the speaker (you may miss the first part of some transmissions). Unless you have interference from an unwanted system that makes it hard to pick up a wanted system it may be best to not program in the tone settings (you'll get everything on that frequency that way).
Other advantages are that some small agencies may have all normal traffic using one tone and a "special" channel programmed with a different tone so supervisors can talk without the others hearing them (yea, this is easy to defeat, but it's a cheap and easy way to get a new "channel" that isn't used much). Remember that most agency radios are programmed by the shop, and users can't make changes so something this easy to defeat may actually work for a small agency.