I can only hope that I don't come off as sounding offensive, as I just want to offer you help.
A really good reputable breeder will allow the foal to stay with the mare until it is four to six months old. As a reputable breeder I have even given 30 days free training, if I've felt the foal was maturing slowly, as they all mature at different levels. The last foal I sold was last year, a filly, that was purchased as a four month old weanling. Sold as a pet becuase in my opinion her head was a little long for showing, she was also very immature, so I left her with her dam until she was six months old and in with the rest of the mares. Mares are the best teachers, then when I did wean her at six months old it was a gradual weaning, I put her in a paddock with the other weanling fillies, and the mares in an ajoining paddock, where no nursing could happen, but babies could still see Moms. This filly was already halter broke, been clipped partially, had her hooves trimmed several times, shots, wormings, bathed, well you get the picture. The buyer did not want her bridle path clipped, so what ever the buyer wants the buyer gets. I also kept this filly for an additional 30 days, since she was going to a home with small children, so that my grandkids could acclimate her to all sorts of sights and sounds and interaction. Such as strollers, carts, flags, balloons, screaming, running up and down the aisles with toy trucks. When she was delivered to her new home she had no problems and fit right in. If your breeder is reputable just ask if you can pick her up at a later date.
On the other hand, in this economy some sellers are bound and determined to sell and the breeder may not want to keep the filly any additional time, so, if your heart is set on this one, go for it. I would recommend to take along an older experienced traveling horse for company. Three months old is even too young for first vaccinations, so filly may get ill, as they need the first one around four or five months and then another in two to three weeks, depending on which is used.
I would ask the breeder some questions such as: Is she halter broke and walks nicly on a lead? Has she had her hooves trimmed? Been wormed if so when? Maybe someone else can offer more advice.