In D&D, you have to bear in mind the definition of a creature's space:
A creature's space is the area in feet that it effectively controls in combat, not an expression of its physical dimensions. A typical Medium creature isn't 5 feet wide, for example, but it does control a space that wide.
Narratively, that means that just because you pull a creature through or into an occupied space doesn't mean that the creature which controls that space is literally in the way at that precise moment.
In fact, because Thorn Whip requires an attack roll (which may or may not be subject to the rules on cover because of the interceding creature's presence), it may be said that the whip goes around the interceding creature because, well, it had to in order to hit the far creature in the first place. In other words, the middle creature is not in the way.
But once the creature is pulled into or through the middle creature's space, the rules are simple:
Whether a creature is a friend or an enemy, you can't willingly end your move in its space.
The creatures are not willingly sharing a space so, for the time being, they do occupy the same space (through no fault of their own).
Once one of the two creatures has a turn, it gets movement and is subject to the requirement that it must move out of the shared space.