It's not a bad thing if a little bit of run off sits in the tray, you just gotta make sure the bottom of the pot is suspended from the water. If the bottom of the pot sits in water the medium will become water logged at the bottom of the pot and will remain water logged until the water in the catchment tray/saucer dries up. If the roots have reached the bottom of the pot, most likely have in your case, those roots will drown and you'll get the death which you see in those pics