We'll talk about a threshing floor in this Mishnah. A threshing floor is where they would take grain and winnow it. They would have chaff flying off it, the thin peel over the grain. They would try to separate it from the actual inner kernel. They would throw the grain up in the air, and then the wind would take away the chaff, which would fly to different areas.
So the Mishnah says, “We have a large threshing floor. We make sure that it's distant from the nearest city, at least 50 amot (cubits).” We want to make sure that when the chaff is being blown away from the threshing floor, it won't blow into the city and bother people, go into their eyes, or cause them discomfort. Likewise, when we're talking about a neighbor's field, the chaff that goes there can also damage the crops.
A person is not allowed to make a permanent threshing floor within his own property unless there's 50 amot of open space on all sides. The reason he does that, as a continuation of the last part of the Mishnah, is to make sure that the chaff from the threshing floor doesn't blow onto his neighbor's plants and plowed field and damage them. So he has to make sure there's a setback, so the threshing floor isn't near the neighbor's plants or property, and there's a 50 amot separation between them.