Those are supposed to be in your inventory. Only keystones go directly into the journal. Fragments you will have to carry around.
Aha! BTW the Journal dont tell us what type of fragments you need for the combines.
The fragments should match the categories. You need fragments of whatever category type you are working within.
Would have helped if we could mouse-ower the items in the journal, to see their names. But guess we will figuere it out without also :)