We are learning Mishnah 2 in the third chapter of Maseches Terumos. The previous Mishnah dealt with someone who separated Terumah from wine, and afterward it turned out that the wine in his possession was vinegar, leaving a doubt as to whether it had turned to vinegar before the separation or after it. Three situations were taught there:
If it is certain that the wine had already turned to vinegar at the time of the separation - the separation is ineffective.
If it is certain that it was still wine at the time of the separation, and it turned to vinegar afterward - this is full-fledged Terumah.
If it is not known when the spoilage occurred - it is a doubt whether the status of Terumah took effect on what he separated.
Because of the doubt he must make a second separation from wine, and he is now left with two vessels: one containing vinegar, and one containing wine. Our Mishnah comes to discuss the law of these two vessels when they fall into chullin.
When only one of them falls in:
"Naflah achas mehen l'toch hachullin - einan medama'atan" - if one of the vessels, whether the first separation, which is now vinegar, or the second separation, which is wine, fell into wine or vinegar of chullin of the same type - it does not render the mixture medumma the way Terumah does. A simple majority of permitted produce is enough, wine against wine and vinegar against vinegar, to permit the entire mixture. Unlike certain Terumah, which is nullified only in one hundred and one, here nullification in a majority suffices, since this is no more than doubtful Terumah.
"Naflah shniyah l'makom acher - einah medama'atan" - the same applies if the second vessel fell into a different barrel of the same type. That too does not become medumma, and it is permitted to drink all the wine and all the vinegar as well, since each fall on its own is nullified in the majority.
"Naflu shteihen l'makom echad":
The law is different when both separations fell into a single vessel. To what may this be compared? To a large barrel in which a blend containing both wine and vinegar together is mixed. In such a case there is no way to measure the permitted wine against the wine and the permitted vinegar against the vinegar separately, since they are already mixed with one another.
Therefore we learned: "medama'os k'ketanah shebishteihen" - the mixture becomes medumma and requires one hundred and one against it, except that we do not go by the total of both separations, but by the smaller of the two.
An example: if fifty liters of vinegar fell in and forty-nine liters of wine, ninety-nine liters in all, we do not require one hundred times fifty but one hundred times forty-nine. The reason: it is certain that at least forty-nine units of Terumah fell in, and against them one hundred times as much permitted produce is required. As for the fiftieth unit - it is possible that the vinegar was the Terumah, in which case fifty units fell in, but there is no certainty about this.
And since the matter is not certain, and the basic requirement of one hundred and one is only rabbinic, we are lenient in this doubt and do not require one hundred against the fiftieth portion. But against the first forty-nine, whose falling in is certain, one hundred times as much permitted produce is required in order to permit the entire mixture to be eaten.
In summary: in this Mishnah we learned the law of two separations that were made because of the doubt about the wine turning to vinegar. Each one that fell by itself into chullin of the same type - is nullified in the majority and does not render it medumma, since this is no more than doubtful Terumah. But once both fell into a single place, and it is no longer possible to measure each one against its own type, the mixture becomes medumma and requires one hundred and one - and we measure according to the amount of the smaller of the two, because only that amount is certain, and regarding the rest we are lenient because of the doubt in a rabbinic law.