This could happen for a few reasons:

• If you recently made changes to the folder, or changed settings for the index, indexing might not be complete. Make sure the indexing status at the top of the Indexing Options dialog box says Indexing complete. (See more How to pause indexing)
• Make sure any file types that aren’t appearing are added to the index.
• Make sure that the folder has the System permission. Most folders already have this, but there are some cases where a folder might be missing the System permission.

To add the System permission to a folder

1. Select the folder in File Explorer, tap or click the Home tab, tap or click Properties, and then tap or click the Security tab.
2. If you don’t see System listed under Group or user names, tap or click Edit.  You might be asked for an admin password or to confirm your choice.
3. Tap or click Add, enter System in the box that appears, and then tap or click Check Names.
4. Under Matching names, choose System, and then tap or click OK until all of the dialog boxes you’ve opened are closed.
5. Rebuild the index.

Via Microsoft.com