
Well a person experienced in dogs would have to be pretty dense not to realise that a bitch is in season (except for bitchesw mating very late as in the example I gave, which is why I advise keeping a bitch away from males an extra week).
No matter how many dogs you have they are unlikely all to be together when the breeder is not there, especially not more than one male with a bitch.
In some breeds there would be no way two males would ever be left together anyway, and even in breeds wehere they get on leaving two males usupervised with bitches would be unwise as conflict can and does occur over girls when they are about to come in season or have recently been.
Accidents like I describe only tend to occur with an untypical season, where the bitches (not the dogs) were hgaving excersise with one of several males at different times.
In Medium to large breeds many small hobby breeders who do not have land and kennel facilities will only keep bitches (as I do) so it is obvious who the sire is. If they have kennels then the dogs will be seperated or maybe with a bitch companion.
If the stud owner has more than one stud dog (increasingly rare) they have nothing to gain from substituting the wrong dog. Most people in a breed can easily recognise the offspring of particular males.
Matings in most breeds are strictly supervised anyway so the breeder can ensure neither is injured and so they know when a litter is expected.
In puppy farms a male will usually be left with several bitches all the time, but the 'producer' will still be aware when they were in season so they can be seperated from the others to whelp.