Is this an 'observation' as you mentioned, or a non-conformance? If it is an official non-conformance (you did mention an ncr), there should be guidance info associated with the NCR in how they would like it closed.
If this is a true 'observation' and it was simply mentioned as an area to improve, I would give the following advice:
Internal audit planning is not performed risk based- If you audit different areas at different frequencies, re-evaluate this based on risk and document this on an internal audit policy/procedure. It could very well be that you only inspect once a month for certain things (building maintenance for example), but high risk inspections (like pre-operational or HACCP point inspections) might be at a much higher frequency. Put this risk based reasoning on a document and make sure the logic is sound.
it is not clear which department audited when on the checklist- I am assuming this means that you do not list which areas/department area being inspected on the inspection form. If that's the case, you will want to update the inspections to define which areas and exactly what are being inspected. It could be something as simple as "Warehouse A-Interior; Warehouse-B restrooms; Building 4 break room" and then break that down with WHAT you are looking for in those areas. Without some type of designation, you will have trouble knowing if you have repeat issues in the same areas, which means you will have trouble correctly solving non-conformance issues.Go to the full post