Identify what the percentage measures
Record whether 99 percent belongs to one stall, a wider cleanup objective or a separate achievement. These should not be treated as interchangeable. The official sources cited below describe the gameplay but do not supply a universal final-item coordinate or documented 99-percent bug.
Inspect the remaining area carefully
Revisit the relevant shelves and nearby objects in a consistent order. View corners and partly obscured items from another accessible angle. Since matching items are selected automatically when shelving, checking the shelf itself may be more useful than cycling the object in your hand.
Keep sorting and optional discoveries separate
Spells, companions, secrets and optional leaderboards exist, but the official overview does not say all are required by every progress counter. Avoid exploration-percentage advice for other open-world games. For a persistent mismatch, share the exact counter and a screenshot in the official discussion hub. Continue with the completion guide or missing-item checks.