Google has always had variations between the [query keywords] results of the “Google indexes” AND the “literal website keyword instances/indexes”; that’s not new, unrelated to search operations aside from the fact that advanced search operators make this more easy to see.

(In fact, the article I linked to references this as a way to do quality assurance on Google’s indexing on content on your own domains.)

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Note that the sum of the counts for the following three queries:

[“aaa” AND “bbb” site:domain.com]

[“aaa” AND -“bbb” site:domain.com]

[-“aaa” AND “bbb” site:domain.com]

...in theory should equal count of this query:

[“aaa” OR “bbb” site:domain.com]

...in practice though, they never have; by never, since Google first released their search results.

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Further, while counts frequently are over 1000, only the first 1000 search results are viewable, and vast majority of searches only pull the first 10 results and review an even smaller percentage of those 10 results.