What compact option did you use? You could try creating a new replica if you can’t remove the deletion stubs. There is a technote on removing stubs as sometimes they can be a pain.
Additional documents you can’t necessarily see at a glance, such as profile documents, documents with readers fields you’re not in, orphaned documents.
You can use “sh database [filename]”, it will give you the information in the third or fourth line.Or you download a tool called “notespeak” (as mentioned before) and open the database within this tool.