Certainly the Lord knew what he was looking for before they brought the scriptures to him. He did not have the time to understand the organization of the records, nor to exhaustively read what was brought to him. He was able to go to the record in question, and note that there was something that was not written. He points this out.
First, the fact that he calls for the records, knowing what he was looking for beforehand, tells us that his purpose in doing this is to highlight the importance of the record of the living oracles. By reading the recent scriptures, Jesus emphasizes them as conceptually equivalent t to the writings of Isaiah he has recently been citing. Not only are the words he is currently speaking important to write down, but those of recent prophets, such as Samuel.
It is not clear from this statement whether only the fulfillment of the Samuel’s prophecy, or the entirety of the prophecy was missing from the record. In this verse we have the Savior only noting that it was the fulfillment of those arising from the dead that was not included.
While we cannot tell precisely what is missing, we can note that the general prophecies were included in Mormon’s text, but neither this prophecy nor its fulfillment made it into Mormon’s plates, save for this mention. For Mormon, at least, the point of the value of the written scriptures was more important than making certain that the record of Samuel was complete.