Late arrivals for Salaat
If you arrive too late at a masjid, and miss the congregational prayer, is it permissible to prayer a second congregation in the same masjid, if there are enough people?
Yes it is permissible. However, it is preferable to do this in a different part of the masjid, such as a separate room. But please note, it is not permissible to miss the main congregational prayers intentionally without a valid reason.
Ibn ul Waqt issue 2, Questions and answers. By Hadharat Shaikh Asif Hussain Farooqui.