Jesus tells the people that he wants to augment their scriptures, so he has Nephi bring them. He declares, “other scriptures I would that ye should write, that ye have not.” One way to read that phrase is that they are supposed to write scripture that they have not written. The other way, and the way that explains what is to come, is that they are to write things they do not have. In other words, “other scriptures I would that ye should write, that [ye do not have].”
One of the reasons it is read as a fault of recording is that the first example is something that they neglected to write. It is not uncommon to suppose that they had neglected anything Samuel had said, but that is not what Jesus says. He specifically says that it was the part about “many saints did arise and appear unto many and did minster unto them.”
They corrected that error. However, Jesus continues. 3 Nephi 24:1 states: “And it came to pass that he commanded them that they should write the words which the Father had given unto Malachi.” These were words that they “had not,” or didn’t have.