no disagreement concerning this, because such a mosque is, by its very nature, intended for separate congregations; it has no regular imam around whom the people gather.
As for the first form—where there are always two congregations in the mosque, the first congregation and the second congregation—then there is no doubt that this is disliked, if not prohibited, because it is an innovation: it was not known in the time of the Prophet, peace and blessings be upon him, and his Companions.
An example of this was what was formerly known in the Sacred Mosque before the Saudi government assumed its administration. There were four congregations in it, each with its own imam: the Hanbali imam would lead the Hanbalis in prayer, the Shafi'i imam the Shafi'is, the Maliki imam the Malikis, and the Hanafi imam the Hanafis.
They would call these: the station of the Shafi'i, the station of the Maliki, the station of the Hanafi, and the station of the Hanbali. But when King Abdulaziz—may Allah reward him خيراً—entered Mecca, he said, “This divides the Ummah”; that is, the Muslim Ummah was divided within one mosque, and this is not permissible. So he united them behind a single imam. This was among his praiseworthy qualities and virtues—may Allah Most High have mercy on him.
Thus, this is one of the harms alluded to: the division of the Ummah.
Moreover, it encourages laziness, for people may say, “Since there is a second congregation, we will wait until it comes.” People then become lax in attending the congregation led by the first regular imam.
As for the second form, it is when this occurs incidentally. That is, the regular imam leads the mosque’s congregation in prayer, but two, three, or more people may occasionally be delayed due to an excuse. This is the point concerning which there is scholarly disagreement.