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Since QGIS 2.16 the attribute tables count the rows starting with 1, on the previous versions it started with 0, so the $ID could match with it. Is this some kind of mistake? Do I have to use another command? Don't really understand the usefulness of this.

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By "count the rows" you probably mean row lables. These does not correspond with features ID at all, they are fixed and don't affect your data - try sort table by some attribute and hover with mouse over the row lables and you will see it.

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So by expression $ID you can get exact actual id of your features starting with 0.

Note: Beware to use $ID in virtual fields, because when you for example delete a feature, this values will set to new actual features id. For more information check this question: QGIS does not show FID field of vector data.

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