One was written in Babylon, and the other was written in Jerusalem (Tiberius, actually, which was where the Sanhedrin was, but it’s called the Jerusalem Talmud because they “should” have been in Jerusalem)
For a really short and oversimplified history, R. Judah the Prince saw that, with the destruction of the Temple and the Roman occupation, the Sanhedrin was losing it’s authority, and he was afraid that the Oral Tradition, which, supposedly, had been passed down from teacher to student from the time of Moses, was going to be lost. To keep that from happening, he and a few other people went to every Rabbi they could find, and wrote down all the oral tradition he could. He then edited the work and that got called the Mishna. (He then died, and you can go to his tomb in Beit She’arim, if you should find yourself visiting Israel any time soon)
But the Mishna is confusing. It’s really concise, and assumes that you already know Jewish law. To make an analogy, it’s like if you were reading about US law, and you read, (from another thread I’m in), “The strict scrutiny test should be used in equal protection cases where race is a factor.” That’s true, and it’s useful, but only if you know what the strict scrutiny test is, and what the equal protection clause is.
So, realizing that the Mishna itself needs explaining, rabbis from all over decided to get together and discuss it, and what it means, and this discussion is called the Gemara. The Mishna and Gemara, together, are called the Talmud. Now, there were two major concentrations of Jews at the time, and two major rabbinic centers at that time, one in the land of Israel, and one in Babylon. So, two talmuds were written, the Jerusalem Talmud, by the rabbis in Israel, and the Babylonian Talmud, by the rabbis in Babylon.
Because there was less persecution against the Jews in Babylon (which was outside the Roman Empire) than in Israel (which was inside it), the Babylonian rabbis had more time to work on their Talmud, which is more complete than the Jerusalem Talmud. Because of that, the Babylonian Talmud became the standard, and nowadays, if somebody says “the Talmud”, and doesn’t specify which one, he’s probably talking about the Babylonian Talmud.
So to answer your question, that’s why they’re different, and there isn’t any controversy over that tractate.