1. The two numbers are measuring different things
Hundreds of wordsBy far the most common. Word counts the entire document; a checker with exclusions turned on counts the document minus the reference list, the citations, or whatever else you asked it to leave out. These are not competing answers to one question, they are answers to two. Compare Word's figure against the total rather than against the counted figure, and the gap usually resolves on the spot.
2. Word's own count leaves things out
Tens to hundredsThe number in Word's status bar is not the whole document. Footnote and endnote text is excluded from the default count, and so is anything in a header or footer. In a footnote-referencing discipline that is a substantial quantity of real writing that neither you nor Word is counting, which matters if your brief counts it.
3. You counted a copy, not the document
Anything from a few words to a whole sectionPasting into a plain-text box drops what a document carries but text does not: table cells may arrive as a run-on line or not at all, text boxes are usually lost entirely, footnote text does not travel, and captions become indistinguishable from body paragraphs. The count is not wrong so much as taken on a different document.
4. The count saved in the file is out of date
UnpredictableA .docx stores the word count Word calculated when it was last saved by Word. If the file has since been edited by Google Docs, LibreOffice, Pages or an export pipeline, that stored figure can be left behind — sometimes badly. It is a record of a past state, not a measurement of the current one.
5. Tokenising rules genuinely differ
Typically a handful of wordsWhat counts as one word is a decision, and different tools decide differently about hyphens, dashes, numbers, symbols and non-Latin scripts. This is real, and it is almost never the explanation for a gap of more than about one per cent. If your two numbers are 2,180 and 2,510, this is not why.