The confusion here is stemming from the compile settings. Going back to the first image of the compile window, to the right of the compile dropdown menu that has “Draft” selected is a funnel icon that is currently enabled (it’s blue in the screenshot), meaning that some of the filtering settings are on. If you click that, the top option there lets you choose what items are actually going to be included in the compiled document. The default setting is “Included Documents”, but you can choose instead to flip that and compile only the “Excluded Documents”, or—as it’s presumably set right now—“All” documents, i.e. compile them all regardless of their “include” checkbox setting.
I’m aware of a bug in the current 3.1.1 Windows Scrivener whereby this setting is not ultimately impacting the results of the compiled document; only the documents marked “Include in Compile” are being compiled. So it would be easy in this case to have changed the setting but forgotten about it since your compile results wouldn’t look any different. That bug will be fixed in the next release. Meanwhile, though, the setting is still (correctly) impacting the compiled word and character counts in the project Statistics, so that’s where the number is coming from.