Coyote dens will be more elpitcal than round, coyotes clean up alot around there denning site, so "most of the time you won't find things/parts laying around a coyote den, fox all the time!! Fox are messy and broadcast there denning site much more than coyotes. Coyotes like areas of easy digging or remote areas with holes already started by other critters, they like a place that offers a good view and scenting of approaching danger, were a fox would den in your sandbox if given the chance LOL!
THe other holes are sometimes dun by pup fox and coyotes, after they emerge and play around the denning site, they will dig around they area, just a natural thing for them to do, when I gas a den I leave these play holes and put traps by them with gland lure or bait in them and come back a few days later and what didn't get gassed will most likely be waiting in your traps. Be it some pups or the [beeep] or male.
Coyotes that receive heavy pressure, will den in some of the most rugged and odd places and finding there dens can be quite a chore. I always carry a nap sack with gas bombs and a tile spade, because if you leave and the pair knows you been in the area, they will move those pups that very night alot of the time or sooner.