I'm currently playing a Warlock (level 7). I picked up counterspell and I have also Psyonic Backlash. I have Gale with me, who also has counterspell. I just wiped out the Githyanki Creche and several times when an enemy cast a spell, when I was prompted to make a reaction, my only choice was the Psyonic Backlash. Couterspell was not an option with either my character or Gale, and yes I had a spell slot available and Gale had level 3 and 4 spell slots available. At first I thought maybe they had spells that are immune to counterspell because they were using new spells I haven't seen yet, but it also happened later with common spells and cantrips I've counterspelled before.
Also, is there something that gives you the ability to make multiple reactions per round or is the AI cheating? When fighting the Githyanki doctor, she used counterspell twice in one round. My character and Gale were on the same initiative. She used counterspell first on my character, and then immediately after used it again on Gale.
Another odd thing that happened, I was hidden and ambushed a group of them. I cast a spell from hiding to start combat, but they cast counterspell. It countered the spell, but I stayed hidden and it didn't even start combat.