I have seen in many mosques that people come late for prayer and having missed the congregation they hold another. Is this practice endorsed by the basic religious sources?
If we observe the practice of the Prophet (sws) and the way he instituted the prayer, it becomes clear that the practice of praying in the second congregation is disliked in Islam. If we disregard the practice of the Prophet (sws) and his Companions (rta) in this regard and allow holding numerous congregations then the spirit of the congregational prayer would vanish. Which congregation is held necessary for Muslims to join? If it is the first one, then the latter congregations become less significant and the practice is bound to develop a tendency to disregard any discipline and regulation in this regard. Therefore, we believe that the view of the Muslim scholars who think that Muslims should not hold a second congregation in the mosques where there is a regular Imam appointed by the government or by the society is very balanced and justified. Islam lays great emphasis on the social and political set-up of Muslims and wants the society to remain united. During the time where there is a legitimate Muslim government which appoints regular Imams holding a second congregation would mean rebellion and would be considered tantamount to challenging the authority of the state. However, these scholars think that there are always exceptions to this rule. In mosques situated on highways, travel stations and hotels and even in the markets, this condition cannot be applied. In these stations, people are actually going through a state of emergency and the prayer timing is sure to be missed. This allowance can be extended to all similar places.
Obviously, just ignoring the prayer and sitting back at home being engaged in worldly activities and later leisurely walking to the mosque and hoping to earn the reward of taking part in the congregation by setting up a second congregation must be discouraged. Those responsible for the management of any mosque can forbid such congregations when they feel that people are being negligent of the duty imposed on them.