Are these experiences from this year? I admit it was a few weeks ago but when I asked my daughter about these groups a few weeks ago she said she had only seen one group and they were well behaved.
Seriously though it does not matter how quiet a group is any large group is going to seem disruptive in a value hotel. At their scheduled meal time they come in backpacks cover the majority of the tables making it difficult to find a place to sit.
I was there a couple of weeks ago and the park was packed with tour groups. They were from many different South and Central American countries (they had the names of their countries on their shirts). In general we did not find them to be really disruptive, but there were some mildly annoying things. Once my daughter and I were headed to the bathroom and a group of about 50 swooped in in front of us. We had to find another bathroom because we were not going to wait for that many kids to use the few bathroom stalls in that bathroom (I don't understand how this is enjoyable for them, either). Once we parked our stroller and came back later to find that a group was lounging around the stroller parking area. Two males in the group were hanging all over our stroller. One of them was propping his feet on it. We were also photo-bombed once by a group when we were having our picture taken by a PhotoPass photographer at HS. We were posing and were suddenly surrounded by about 35 smiling young people who wanted their picture, made, too. It took the photographer a few minutes to explain that they could have their picture taken, too. Just not with us. When we were getting our annual passes activated at guest services we had to wait quite a while because an entire group was waiting in line at guest relations. CMs were trying to find out if they all needed something or if the CMs could just communicate with the leader. There seemed to be a lot of confusion. Finally a couple of CMs came over and herded them over to a different area to help them.
We definitely saw clapping and chanting. Once in line for Living with the Land. My daughter and I held back for a few boats after they finally got loaded because we didn't want our peaceful ride to be disrupted by chanting. I don't think they actually ended up chanting on the ride itself, but I didn't want to take that chance.
I understand how some people see the clapping and chanting as an unoffensive exhibition of enjoyment, but it really does negatively affect my enjoyment of the park because part of the joy of Walt Disney World is the music. I like to hear the joyful music being played over the speakers as I walk thru the different areas of the park. When I am at a sports arena, I expect to hear cheering fans. I really prefer not to hear that at Disney. Sometimes I feel like bursting out into a joyful rendition of Zip a Dee Doo Dah myself, but I refrain because I really do believe that would bother some other guests. Imagine if all 40,000 of us in Magic Kingdom began expressing our joy however we liked!
As to how Disney stops it, I really don't know. Civility in public places often depends on people policing themselves and adapting their behavior to cultural norms. When you have a society like we do today, where there are so many different cultures and few norms, there are naturally going to be some issues.