Here is another fascinating Mishnah - Mishnah 8 in the fifth chapter of Tractate Terumos.
The case in the Mishnah:
One unit of Terumah fell into one hundred units of chullin. Before the owner of the mixture managed to remove a single unit in order to give it to a kohen, a second unit of Terumah fell in. The result is that there are now two units of Terumah against only one hundred units of chullin.
The opinion of the Tanna Kamma:
The Tanna Kamma holds that once there is no longer one hundred against the Terumah - "hakol asur" - everything is forbidden. The Bartenura explains his reasoning: we view the matter as though both units fell in at the same time. We do not treat the situation as though one unit fell in, thereby permitting the entire mixture, and only afterward a second unit fell into a mixture that had already been permitted.
The opinion of Rabbi Shimon:
Rabbi Shimon permits it, since it is enough that he remove two units. In his view we regard the matter as though one fell in and afterward another fell in, and this fits neatly with Rabbi Shimon's well known principle elsewhere: if a person intended to remove the unit from the mixture and simply had not yet managed to do so, it is as though it had already been removed, and all that remains is the technical matter of actually taking it out. According to Rabbi Shimon, the Sages were lenient in such a case, and if an additional unit fell in, he removes that one as well.
It is worth remembering that we are nowhere near the boundaries of a Torah prohibition; the entire discussion is rabbinic. According to Rabbi Shimon, the rabbinic requirement of one hundred times the amount of Terumah is set aside, if you will, when a person is in the middle of removing the unit and in the meantime another one falls in - and everything is fit for use. That is the content of the Mishnah.
The qualification of Rabbi Elazar the son of Rabbi Shimon in the Tosefta:
The difficulty arises from the words of the Tosefta - a Tannaic source contemporaneous with the Mishnah that comes to complement it. There a statement is brought in the name of Rabbi Elazar, the son of Rabbi Shimon bar Yochai (the son who was with him in the cave for thirteen years): all of this applies only on condition that he knew about it, that is, that he knew the unit had fallen in.
The approach of the Bartenura:
According to the Bartenura, this qualification refers to Rabbi Shimon: Rabbi Shimon permits the mixture even though a second unit fell in, because he knew about the first one falling in and stood ready to remove it, so that all that remained was the technical matter of carrying it out. His awareness of the mixture is what creates the effect of nullification, and it allows us not to cross the threshold of one hundred to one that would render the mixture forbidden once the second unit fell in. Put differently: we do not consider it as though everything fell in at once, because he was aware of the first unit falling in and intended to remove it even before the second one fell. And nevertheless the Bartenura concludes: "and the halachah follows the Sages."
The Rambam's approach:
The Rambam, apparently, understands Rabbi Elazar the son of Rabbi Shimon's qualification differently - as referring to the first opinion: the first opinion holds that the mixture becomes forbidden when the second piece falls in, unless the person already knew about the first one falling in. For if he knew about the first before the second fell in, the first had already become nullified and the mixture had become permitted, and when an additional piece falls in, what we have before us is still a permitted mixture.
This is similar to the previous Mishnah, where we learned that as long as the line is not crossed at the moment a new piece falls in, that piece is nullified as long as the required quantity is present. It makes no difference that we are drawing closer to the forbidden ratio, and even though in the end the ratio of one hundred to one was exceeded - provided that at each and every stage there was a valid nullification.
According to the Rambam's understanding, then, the prohibition applies specifically in a case where the person did not find out about the first piece falling in before the second one fell, and therefore we view it as though both fell in together. But if he did know - it is not as though they fell in as one. Accordingly the Rambam rules: if one piece fell in, he found out about it, and before he managed to remove it a second piece fell in - the mixture remains permitted. And this, apparently, is the practical halachah, since the halachah follows the Rambam.
In summary: regarding two pieces of Terumah that fell into one hundred of unconsecrated produce one after the other, the Tannaim disagree: the first opinion forbids the mixture, because we view both as having fallen in together, and Rabbi Shimon permits it, because his intention to remove the first piece is treated like an actual removal. Rabbi Elazar the son of Rabbi Shimon's qualification in the Tosefta - that everything depends on knowledge - is explained by the Bartenura as referring to Rabbi Shimon (and the halachah follows the Sages), and by the Rambam as referring to the first opinion, and from here that the practical halachah permits the mixture when he found out about the first piece falling in before the second.
It is worthwhile to go back and listen to the Mishnah once more; it will not be repeated here, since everything that needed to be said has been said. Hopefully these matters are clear.