That's kind of a stupid answer from your vet.
Yes, it is likely that she knows where the box is. What she doesn't know is that she's supposed to use it every single time, or she may not feel like going all the way to the box.
Usually with young kittens one box isn't sufficient, especially when you don't have other cats showing them correct behavior. Their attention span sucks and if there's not a box within close proximity and they really have to go they will have accidents. It may take a fairly long time for them to completely train. Some kittens catch on immediately some are slow learners.
It would help to have several boxes. Put them where she's likely to have accidents (corners are a common place). I usually move some used to litter to new boxes to get the smell in them (doesn't have to be dirty, just from a box that has been used, it will have enough smell), otherwise young kittens sometimes don't realize what they're for. The smell is often what will trigger them to use it, so also make sure to clean any spot they've had an accident really really good.
You also might try scooping the boxes several times a day, whether there's anything in them or not. It seems like cleaning the litterbox triggers them to use them. At that point you can give them a small treat for using it.