Unless you have caught thousands of pokemon and have documented proof, there's no way with your sample size to prove BMS isn't working. BMS does not guarantee that every 1/4 pokemon you catch will have H/A. You've simply been unlucky.

 

I was farming magnemites yesterday and my first 32 encounters 24 were sturdy, 4 were Magnet Pull and 4 were Analytic. Magnet Pull has the same likelihood as sturdy. Analytic is only supposed to be a 5% chance (without BMS). Nothing is guaranteed.

25% to meet a h.a pokemon, always 25% each time, so itsnot 1/4, just like 5% to get a spooky pikachu, i met 96 pikas and no spook.

I kept hunting Pokemon untill bms ended... From what i got i saw numbers usually seen without an active medallion, no more, no less.

I can't say for sure this is a bug, but no doubt this is strange and makes me think that something was not working as intended, so i wrote this topic.

 

(I edited first post)