Okay, I tried to play this flaws with my players but eventually we all forgot about their very existances. Right now I think two or three of my players have this flaw but I don't really know what to do with it as a storyteller.
So i'm asking, how do you handle the magical animal compagnon flaw and his mundane counterpart in your Saga and what kind of stories they can be included in ?
We used it foremost as somethinig described by the characters player during character generation. As the SG I've often played the 'companion' - and both the interaction with the character as well as the actions of the companion can add certain elements, themes or moods to a session, and at times influence the plot.
As an example we've got an apprenctice (PC) with a magical cat - to everybody else its meows sound as any regular kittens, but to her it is understandable, leading to a lot of dialogue only perceptible to others as monologue (and meows). At times the cat makes things clear to the apprentice she wouldn't otherwise have known - sometimes things her master doesnt even know - and in that sense it is a perfect tool to keep the apprentice as much in the story, and not just floating at the edges of a sessions main plot, and at other times it leads her into terrible trouble.
Maybe someone should give one of those out to someone who doesn't read the rules...a knowledgeable cat that is...
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One of my players took the magical companion version, and I intend to use the animal as a potential source of story hooks. The crow will go off one day, and return with news that he spotted something of interest. It could also return wounded due to an encounter with another magical beast... something the characters will then have to deal with.
On a day to day basis, I'm using the crow as a bit of comic relief. I play it's voice, and the little bastard is quite the curmudgeon.
The player will eventually turn the crow into his familiar, I would surmise.
Due to the fact that the animal does not have the benefit of the player's parma yet, it may become a target should the player's Enemy flaw happen to show up at an inopportune time.
What kind of characters are the mundane companions?
Have they chosen the animal companion?
Which animals did they choose?
If 02 or 03 players have this flaw , i would find a thematic link as to why they all have it.
Which Realm are the animals aligned with? (I'm guessing no-one picked Infernal). 
Thanks for the replies it was really helpful.
To Ravenscroft :
Two out of four of my player's mages choose this flaw.
One with the magical animal compagnon (vulture) and the other one the mundane kind (didn't choose, expecting to find it in-game)
Hard to find a connection or a thematic link but it gives me some ideas. 