It did happen. Ic ould give you some exemples. It's not fiction. If the mother was more prestigious the kids inherite her name.
The Georgian Bagrationi for exemple. The sons of Tamar Bagrationi were Bagrationis.
If you don't know anything about the topic it would be better to don't say anything insteed of spreading false informations.
Your example isn't a matrilineal marriage. And I could tell you the same thing about posting false information - since it didn't happen. Seriously though - relax. Why jump to the gun? There was humour in there - and funnily enough I got 2-5 votes for saying something which was at least intended to be pretty close to what Me_ said, who got a 7-1 vote

. So maybe my joke wasn't brilliant or easy to get, or the part which was serious was too strong, but of course I had a reason for it? Or what did you assume?
There are several examples of people picking their mother's last name (including non-marriage ones) or other types of last names. Hell, there are even examples of people being member of several dynasties at the same time, or those who were regarded to be a little of each, not to mention those who changed names during the course of their life. So all of the CK2 dynasty/house limitations are already fundamentally broken to begin with - they don't come close to fully describing history. It's a weird approach to start describing history with CK2-terms. The whole dynasty thing is a also bit of a loose goose to begin with (lots of modern classifications tucked in there), so how could then a strict matrilineal marriage system be built on it if that foundation isn't even there. I'd argue not even the patrilineal marriage works with that in mind.
To be honest, I'm not even sure exactly what the original poster's question means - of course history was not exactly like CKII where there was a matrilineal marriage. You'd need written records proving this was a property of the marriage itself (not derived from the children's choice of dynasty since that's another thing, even if those things can coincide). Then you'd also have to show of course that what they mean by matrilineal (using that word exactly) is exactly what we have in CK2. E.g. "Person X and Y are hereby married matrilineally before God, thereby granting assurance that their children will therefore be of the mother's dynasty (XYZ).." or variations thereof. Anything less than that and you haven't, or anything more and you haven't..
I'm no history professor, but from what I read in history books (which I do read from time to time), I've never once seen anyone lay forth evidence of some sort of matrilineal and patrilineal division as a property of the marriage itself. There are just plain marriages, with or without conditions/dowries/dowers/mortages/etc/tc and all of that, but no such things as a matrilineal marriage. So it's not like my opinion is completely unfounded? That said, perhaps there are things I have yet to read where precisely this thing exists, so I could be false. But even then, since this isn't a elite research forum, I retain my right to be (unknowingly) incorrect.