How did all the prophets pray in congregation behind the Prophet Muhammad, peace be upon him, in Al-Aqsa Mosque on the night of Al-Isra and Al-Mi'raj, given that the mosque's capacity is only about 5000 people?

It has been authentically established that the Prophet (peace be upon him) led the prophets in prayer in Jerusalem, and the more apparent view is that this occurred after his descent from the heavens.

There is a difference of opinion as to whether he prayed with all the prophets or with a group of them. The روایت (narration) agreed upon for its authenticity states that he prayed with a group of them, as he led Musa, Isa, and Ibrahim (peace be upon them) in prayer. While another narration in Ahmad states that he prayed with all the prophets, the authenticity of this narration is disputed.

And assuming that he prayed with all the prophets, the more correct view is that he prayed with their spirits, visualized in the forms of their bodies. The world of spirits is part of the unseen, which we do not know, and Allah is capable of all things. Thus, there is nothing to prevent the gathering of spirits in a place that cannot accommodate many bodies.

So, the Messenger (peace be upon him) saw the spirits of the prophets visualized in the forms of their bodies, and this does not contradict seeing some of them praying in their graves.