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First, it can be the fact that they’re just simply better than you.
Second, there are a lot of ways to counter vac. I’d say the first and best one is proper teamwork. Pressure them with hitscan and projectile classes in the same time.
Second, you can find its weak points. Simply, the fact that the vaccinator won’t be able to buff them (implying you’re smart enough to not let them have critheals in fights) can get your team to take and win every 1v1. It gives your players a buff advantage. Play heals, play buffs.
Some people would say running pyro to mid can be a good counter but I’m not really sure about it.
Anyway, you also have the simple fact that you always have an advantage (Uber > Vaccinator). Basically when pushing with uber against vacc you will have 2 players which you won’t be able to hurt as much (Obviously, the medic + his target) So you need to ask yourself: Do i throw my hitscan & projectiles on THESE 2 players, or do I focus the players who actually dont really get vaccinated? Thats up to you;
also the usage of vaccinator can really be punished by simply pressuring them. For example, a medic with a vaccinator would feel more comfortable standing near choke points rather than a normal medic. And the spam can cause him to repediatly use his vaccs.
That’s all I can say.

Keep the pressure up. All the time! Vaccinator really sucks at giving actual heals, so you need to win a war of attrition by just spamming them down real hard. This might sometimes mean your opponents have a better start at mids, but as their health numbers go down, your own heals become stronger and stronger.

Also try to fake them out a bit: Fake a push, commit just enough to make them use a bubble, then fall back for a step or two so the bubble fades before they can do anything to you. This obviously requires a high level of diligence and teamwork, but it’s not much unlike forcing normal ubers out of your opponents without using yourself. It might actually be easier because using a bubble is far less an investment than popping a full uber. Plus, shitty buffs in the first place.

On the other hand, when you have to deal with the Vacc combo, use different dmg types – don’t bring in demo and gunboats soldier! Take scouts and demo/soldier, heck, your solly might even be able to just melee the medic! (also, market gardener, as DD pointed out)

Have you tried aiming, works well.

their medic is barely able to buff the flank, focusing them means free kills in the uber push, if they are out of reach going with a soldier, scout uber while the demo is behind your medic and spams as well.