Possible meanings are 1) the word "iniquity" refers to the actual acts of iniquity, or 2) the guilt that God attaches to iniquity, or 3) the punishment God will give for that iniquity.
Yahweh speaks of his own remembering Ephraim's iniquity as if he were a scribe who had written down a record of them, rolled up the scroll, bound it, and put it away so he could show it to people in the future.