The DM decides how high Evard's Black Tentacles can reach (and 0 feet is a valid ruling)
The text of Evard's Black Tentacles says (emphasis added):
Squirming, ebony tentacles fill a 20-foot square on ground that you can see within range. For the duration, these tentacles turn the ground in the area into difficult terrain.
So the wording of the spell clearly specifies that it affects an area on the ground. For creatures running around on the ground, it is easy enough to determine whether they are in the area: if they set foot on the affected ground, they have entered the spell's area. For creatures flying "at ground level", i.e. occupying 5-foot cubes at the same level as non-flying creatures, the situation is a bit more ambiguous: obviously the tentacles must have some length in order to grab onto anything, but it's unclear how long they are or how far up they can reach, by RAW. Notwithstanding the portrayal of the spell in most art, it's entirely possible for the spell's effects to be caused by knee-high tentacles, or perhaps long tentacles that writhe across the ground until they find a creature to climb up onto.
I tried to find some guidance in the other surface-affecting spells, but the only other spells I could find that specifically affect a surface rather than a 3-dimensional area are Entangle, Grease, and Earthquake. Of these, Entangle is no help, since it has a wording very similar to Black Tentacles, complete with the exact same ambiguity about height. Grease and Earthquake, by their natures, unambiguously affect only creatures in contact with the ground, but not for reasons that provide any guidance for Black Tentacles or Entangle. So ultimately, it's up to the DM to decide how high the tentacles can reach, because the spell doesn't specify.
Were the creatures actually flying?
As Mark Wells points out in the comments, just because a creature has a fly speed doesn't mean that creature is continuously flying. Especially if the creature flies using wings (as opposed to levitation or some other means), flying takes energy, and the wingbeats might make a lot of noise. A typical flying creature probably wouldn't be flying while holding a conversation on the ground. And if these creatures were hovering just above the ground instead of standing, ideally your DM should have mentioned that when describing the scene.
It's possible that your DM didn't know you had a spell that (maybe) only affects creatures on the ground, and so they didn't know that detail was important, in which case it would be good to give the DM the benefit of the doubt. It's also possible that your DM thought the spell was "cheap" and was looking for any excuse to wheedle out of it. I don't know your DM, so I can't tell you which it is.