Such a problem with the early Colt's Frontier Six Shooter
might have occurred because of the firing pin hole in the recoil plate being too large, or some type of mismatch between the pistol and the Winchester ammo (possibly something to do with the size or softness of the primer cup. Hadn't heard of such, however.
Remember that the .44-40 in the Colt's wasn't availabe until 1878-79, so most of the Rangers, who had to supply their own guns (IIRC), probably wouldn't have replaced their SAA's in .45 LC very readily.
So far as packing a rifle in .44 WCF and a pistol in .45 LC is concerned, that could, AND DID, lead to some serious problems with mixing ammo. In one documented instance Ranger George Lloyd got in a firefight with some Indians. In his excitement, he got a .45 round in his Winchester '73, tying up the rifle!
Fortunately, the rifle was a '73, and he was able to use his pocket knife to remove the sideplates and the offending round, before getting back in the fight, which he survived! Of course, the earlier Winchesters/Henry were in .44 Rimfire, but had he made that mistake with either, it would have taken at least fifteen minutes to get the .45 round out. Trust me on the timeline...I KNOW from personal experience, fortunately at a match, and not in a firefight!