Dwarfism in Miniature horses is a complicated matter, usually involving several different mutations of the same gene (known as D1, D2, D3 and D4). A horse has to inherit defective copies from both parents to be a dwarf. If this baby was sired by the stallion that also sired the dwarf foal, you know the stud has one of the above (almost certainly not D1, since it seems that when D1 is combined with anything other than the normal form of the gene (N), it results in early-term death of the fetus). If your foal is indeed a dwarf, she got one defective gene (probably D2 or D3) from her sire, but she had to get one of the D's from her mother, too, which is why I asked if she had been tested.
There are many degrees of dwarfism. In the worst cases, the foals are so deformed that, even if they survive being born, they usually get put down for humane reasons. The least affected may just be rather awkward and dumpy looking, but tooth problems and leg/hoof problems can make them high-maintenance (to say nothing of the digestive issues that can crop up). An underbite is one of the most common issues seen in all types of dwarfs. Some dwarf foals are born with an underbite, in others, it develops as they grow. Severely misaligned jaws can make eating difficult to impossible, but even a slight misalignment means teeth that don't wear properly, and it will take frequent floating to make sure the animal can make the best use of its food.
The fact that the vet didn't say anything specific about dwarfism may not mean anything. Unless he has a particular interest in miniature horses, he may not know much about dwarf minis.
