Hi Arzhell, and welcome to the forum.
When users report issues with word counts, I recommend checking four items.
Are the Documents Children of the Draft/Manuscript Root Folder?
The first thing to review is to make sure that all the documents you’re expecting to see in the word counts are actually set up as children of the Manuscript or Draft root folder in the project.
A quick way to confirm that is to click on the small chevron to the right of the Draft/Manuscript root folder to hide its contents.
If you hide its contents and the documents are still visible, then they’re not counting because they’re not a part of the actual manuscript.
You can use the Documents > Move To options to move them to their correct positions.
Are These Documents Marked “Include in Compile”?
If all the documents do hide when you click the chevron, then their word counts should be included.
Since they aren’t being counted, you’ll want to check either the lower right edge of the main editor or the Metadata tab in the Inspector panel to verify that each of these documents is marked as “Include in Compile.”
Along the lower right edge of the main editor, you’ll see a document-shaped icon. If it has a checkmark on it, the document is included in the compile.
If it has an X, that document is not being included in compile. Clicking that icon should mark it as being included.
Re-indexing the Project
If everything is in the right place and marked as included in compile, the next item to test is to re-index the project. Please use the File > Save and Rebuild Search Indexes command in Scrivener. (For any Mac users who see this post, you’ll need to hold the Opt key while clicking on the File menu to see this command.)
Scrivener should show a small panel where it runs through all the documents in the project to check their contents.
That might be enough to correct the word counts.
You could use Project > Statistics and change the “Estimate (Faster)” option to “Accurate (Slower)” before doing this and then use that command afterward to see what that does to the total word count in the project.
Has the Project Been Compiled Recently?
If all the documents are marked as being included but the word counts still are not right, have you recently compiled only one part of your manuscript?
You can use the File > Compile panel and check that the Draft/Manuscript root folder is selected at the top right of the compile settings and that these documents are showing there.
You might then compile again to see if that fixes the word counts.