2 things, though I could list more depending on the church/denomination...
1- When I was younger, I hated all the singing. Boring. I know they are not singing for me, or to me, and it's not about me... but still. Now, most all these churches have ditched the choir in favor of "bands" (or a combo in some cases). It has made me miss when it was just the choir. Some places are not as bad as others, and I seem to be a small minority who can't stand it, but man it grates me.
2- I'll admit upfront this is a weird one, but I hate the, "everyone turn around and say hi and good morning to the people around you!" I don't know if that's just a thing in the south or what, but I've been to multiple places that do it. So awkward. And for someone who can say some wildly inappropriate things at the most inappropriate times, it's best that I'm not encouraged to interact with people I hardly know (or don't know) in a church setting.