My gut feeling tells me that lots of runs, chomps, and mangled bullheads are the result of “other” fish- channel cats, walleyes, etc and not flathead cats. This is hard to prove unless you actually connect with these “other” fish which sounds like you did RB.
I believe when a flathead is hungry, they eat. Ever watch fish on a camera, in an aquarium? When they eat, they flare their gills and suck their pray into their mouth. I’m convinced flatheads are no different but they move a ton of water when they suck their prey in, which creates the telltale “thump”.
I caught a little 9 pounder the other night that thumped, pulled 3 short clicker bursts, and then I set the hook and landed it. I hooked the fish good, and upon closer inspection revealed the bullheads tail just protruding out of its throat. Just proves to me that it doesn’t take very long at all for a flathead to get the bait in its mouth and heading down its throat. This is why I believe those mangled bullheads are hit by something else.
I also believe that we get a lot of “false” runs while flatty fishing that may lead us to believe we are having more activity than we really are. I know that the clicker on my 7000s will not hold when a small amount of debris (weeds, leaves, etc) starts to accumulate above my sinker while fishing in decent current. This is even worse with a 6500 which has less clicker tension. A chunk of bark or small piece of wood floating by underwater is definitely enough to cause a run as well. I still treat these “false” runs like fish but can usually discern that it isn’t a fish after a few seconds. If there is still any doubt, I’ll set the hook just in case. Better safe than sorry. Typically the hookset is enough to pull the bullhead off and you reel up thinking you just lost a fish because your bait is gone.
I guess my point comes back to what was mentioned earlier and that is too clearly identify whether or not that is really a fish before you set the hook. Hooking percentage will go waaaaayyy up if you know you are setting into a fish vs setting into a clump of grass, bark, or a channel cat with your baits tail in its mouth.
Just my deep thought for the day.