Repeating commonly used phrases is not plagiarism.
Not conforming to a specific citation style is not plagiarism.
Making a reference or allusion to something generally known (like throwing in a Bible quote without quotes or citing verse and chapter) is not plagiarism.
Not citing a source for every single fact invoked is not plagiarism.
Sloppy paraphrasing practices get a red pen from the professor, but are generally just bad practices and do not reflect an intent to deceive or, specifically, an intent to pass off someone else's words or ideas as your own without due credit. There are degrees, but if it isn't rampant and extreme, it's more akin to bad copy editing than intellectual theft.
If you run every academic's dissertation through one of these programs, you'll almost always find "plagiarism."
Expectations about citations differ depending on a variety of factors and change over time. Popular history books used to have fewer references/end notes (generally), now they tend to have a lot! This is partially just a style change, and partially a response to some "making things up" scandals.
The clearest example of plagiarism: uncredited ghostwriters, but we all accept that for some reason.