First note, there are a number of BVH Tree specializations. The more common ones exclude intersection of bounding volumes from neighbor nodes (i.e. Left Box cannot intersect Right Box).
Now the whole point of a bounding volume is that it bounds the underlying object. So if that object has a transform that scales it past the bounding volume, then that means the bounding volume is NOT a proper bounding volume (BV).
Two ways to fix this, if the bounding volume was computed on untrasformed geometry, then when checking ray-boundingVolume intersection, first transform the BV to the same coordinate system as the object.
Depending on what you're doing, a more efficient way may be to compute the BV directly on the transformed object (Scaled, translated, etc) object. This way you don't need to transform the box (or the ray) when doing initial ray-BV check.
Hope that helps.