All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
Scholars held different opinions regarding the Rak‘ahs of the prayer caught along with the Imaam by one who joins the prayer late. Is it the beginning or end of his prayer? They have three opinions regarding this. The reason behind their disagreements is that it was mentioned in some of the narrations of the well-known Hadeeth: “Whatever you catch up with, pray, and whatever you missed, complete it.” [Al-Bukhari and Muslim], and completing entails that what he has caught is the beginning of his prayer. In another narration, he, sallallaahu ‘alayhi wa sallam, said: “Whatever you catch up with, pray, and whatever you missed, make it up.” [Abu Daawood, An-Nasaa’i, Ahmad and Ibn Hibaan designated it as Saheeh], and making up entails that what he has caught is the end of his prayer. Imaam Abu Haneefah and Imaam Ahmad according to the well-known opinion of their mathahib (i.e. schools of thought), adopted the narration of “make it up” while Imaam Ash-Shaafi’i and some other scholars adopted the narration of “complete it”. Imaam Maalik acted upon both of them. He applied the narration of “complete it” to the acts and the narration of “make it up” to the words. To explain, we may apply this to the one who catches one Rak‘ah of the Maghrib prayer along with his Imaam, he should then offer two other Rak‘ahs along with reciting Al-Faatihah and a chapter of the Noble Quran in each and he should sit in between. In doing so, as he makes up for what he missed, he has adopted the narration of "make it up" for the words he missed (by reading Al- Faatihah and chapters of the Quran) and adopted the narration of "complete it" in terms of the actions (by sitting in between the two Rak‘ahs". This is the opinion adopted by Imaam Maalik . Ibn Rushd deemed it weak because it entails that some of the prayer will be completed while another part will be made up.
According to what was previously mentioned, whoever catches two Rak‘ahs with the Imaam in ‘Ishaa’ prayer should complete his prayer in a low voice and what was caught with the Imaam is the beginning of the prayer. This is the most preponderant opinion for two reasons: First, the narrators of “complete it” are greater in number and memorization than those who narrated “make it up”. Second, "making up" in the narration refers to accomplishing the action and not to the well-known technical meaning of making up (i.e. compensation). This is because the technical meaning was made by late scholars of jurisprudence while, when Arabs speak about making up, they mean doing the actions.
Also, the statement of the Prophet, sallallaahu ‘alayhi wa sallam, “And whatever you missed” implies proof of this because the meaning is that whatever you missed of your prayer, not from the prayer of the Imaam and what the follower has missed from his prayer, is the end of it.
However, whoever adopts the other opinion cannot be blamed for doing so because scholarly disagreements in this matter are to be taken into account and every party has its evidence.
Allaah Knows best.