Technically? What, did they think Bron was some kind of ghost communicating with the living and the father thing was just a guess? Wow.
But that does bring up a theory I had. Not sure how much sense it'll make, but here it goes: What if Bron was not the father? In the flashback, Bron indicates he only knew of one offspring; he never says that he's trying to find "his children"; instead he's just saying he's trying to find his "one child".
Maybe longnecks typically only have one child born, maybe to reduce the energy needed to lay and hatch them, something like that. But suppose a female is courted by more than one male. We see this behavior in cats too; the females can give birth to kittens that have more than one father. Maybe the same is true for dinosaurs as well.
Maybe Littlefoot's mother was courted by another male. At this point, she might have thought she'd never see Bron again, so she allowed another male to approach her, perhaps thinking he would stay with her to help out. Whether or not he abandoned her or was killed, I don't know, but the result is that she's alone again, eventually finding her parents and living with them, and pregnant with more offspring.
Now when I said that longnecks may "typically" only have one child born, there may be exceptions to this rule and maybe they have more. Perhaps she had two children from Bron and two children from the other longneck. If memory serves me right, in the first movie, Littlefoot would have had 3 siblings had they not been smashed.
What if it was Bron's kids who were smashed before they were hatched? And only one of the other longneck father's children was smashed, leaving only Littlefoot? Perhaps Bron isn't Littlefoot's father in this case, but this mystery longneck who completely vanishes (killed or just abandons them).
Littlefoot's grandfather may have only guessed Bron was Littlefoot's father. The eggs would have looked the same, and it would have been hard to tell who fathered what egg. Grandpa Longneck may have thought Bron was the father due to the similar coloration between him and Littlefoot, but appearance alone doesn't make a father and son related; it's at a genetic level. I mean look at Cera and her parents. She and her siblings are all pale yellow while her parents are gray. They certainly don't look related, do they?
Do I believe this notion of Bron not being the dad? Not really. I do think that chances are, Bron is Littlefoot's father. But if someone wanted to believe Bron wasn't Littlefoot's real father, well, this is one way this scenario could have happened.