Tons of my friends have had the same bad luck and noticed the counter teaming too so I'm certain that is a thing that happens in the Maison. After all the final trainer teams will stay the same, but the trainers you have to make your way through to get to them won't, meaning they can easily change their Pokémon to counter yours.
It's true. Noticing the counter strategies is very easy, I remember when I was up against a Latios that had Thunder which somehow hit every time plus my team didn't match up well with it at all.
Yesterday I recall having my Mega Altaria up against a team entirely of Poison-types. It must have known she gains Poison weakness when she Mega Evolves so the trainer must have tried to prepare herself for it. I do at least use her as a secret weapon for breezing past early trainers before forfeiting at tougher ones solely so I can collect the BP I had gotten leading up.