Playing as Ellie, you will encounter journal interacts through the game. You will also find existing entries in the journal from Ellie's journal. Ellie has multiple journals throughout the story & all should be considered separate. This means that journal entries you have as younger Ellie in a flashback will not be found during present day gameplay.
However, if you do find that you are missing journal entries from the correct timeline, or find journal entries from flashbacks in present day; those are bugs & should be reported through a support ticket.