There are many that have been a part of our fellowship who we called brothers who have left us, in which this verse is referring.
(1Jn 2:19) They went out from us, but they were not of us; for if they had been of us, they would have continued with us; but they went out that they might be made manifest, that none of them were of us.
I can say looking back at many of those that I knew well who left us, that we never were completely of one mind. There were always issues going on, but we were patiently waiting to see if God would work it out with them.
This is confirmed in the Old Testament through the “mixed multitude”. These were those from other nations that came out of Egypt with Israel, but were not truly of Israel. They were a part of Israel for a long time, but eventually their fruit was manifest and they began to long for Egypt. The rebellion and complaining started with them and then spread to the children of Israel.
(Num 11:4) Now the mixed multitude who were among them yielded to intense craving; so the children of Israel also wept again and said: “Who will give us meat to eat?
(Num 11:5) We remember the fish which we ate freely in Egypt, the cucumbers, the melons, the leeks, the onions, and the garlic;
(Num 11:6) but now our whole being is dried up; there is nothing at all except this manna before our eyes!”
It was not until the walls of Jerusalem were being re-built in Nehemiah that the book of Moses was read and the people realized that the mixed multitude must be separated from Israel.
(Neh 13:1) On that day they read from the Book of Moses in the hearing of the people, and in it was found written that no Ammonite or Moabite should ever come into the assembly of God,
(Neh 13:2) because they had not met the children of Israel with bread and water, but hired Balaam against them to curse them. However, our God turned the curse into a blessing.
(Neh 13:3) So it was, when they had heard the Law, that they separated all the mixed multitude from Israel.
We have recently been shown by God more clearly how the Body is to function with every member doing their part, and those that disagree with this Godly order are the mixed multitude who came with us out of Egypt. They continued with us for a while, but when this part of the book of the law was read and applied it became clear that they are not of us. They never agreed with this doctrine and God only just now made this manifest. This is just one of many siftings that have taken place and there are many more to come to manifest who is approved of God and who is not.
The wheat and the tares grow together until the harvest, and we never know when that harvest will come. The Lord will seek occasions and manifest the tares among us in the fellowship and within our own lives as he sees fit.
(Mat 13:27) So the servants of the owner came and said to him, ‘Sir, did you not sow good seed in your field? How then does it have tares?’
(Mat 13:28) He said to them, ‘An enemy has done this.’ The servants said to him, ‘Do you want us then to go and gather them up?’
(Mat 13:29) But he said, ‘No, lest while you gather up the tares you also uproot the wheat with them.
(Mat 13:30) Let both grow together until the harvest, and at the time of harvest I will say to the reapers, “First gather together the tares and bind them in bundles to burn them, but gather the wheat into my barn.” ‘ ”
(1Th 5:1) But concerning the times and the seasons, brethren, you have no need that I should write to you.
(1Th 5:2) For you yourselves know perfectly that the day of the Lord so comes as a thief in the night.
(1Th 5:3) For when they say, “Peace and safety!” then sudden destruction comes upon them, as labor pains upon a pregnant woman. And they shall not escape.
(1Th 5:4) But you, brethren, are not in darkness, so that this Day should overtake you as a thief.
For this reason we must diligently pray and search our own hearts and minds to see if we are in the faith lest we be taken away in rebellion.
(2Co 13:5) Examine yourselves as to whether you are in the faith. Test yourselves. Do you not know yourselves, that Jesus Christ is in you?—unless indeed you are disqualified.