I guess I'd have to start with where are you, what would you expect, what's your source of information, what transmitter are you on, what muxes are you finding, and so on.
It sounds to me like you're picking up muxes that you shouldn't - remember, they're just carrier signals in the old analogue frequencies, so if you're in an area that always had "ghost" channels or in which you could choose to orientate your aerial towards one of a choice of transmitters then that may be the issue now.
tvheadend will simply report what it's found (assuming you have autodetect enabled). It may be that you've got the right muxes in there somewhere, and you simply need to disable the ones you don't want so that service scanning and channel mapping will work with what's left.