Why did she take my resignation badly?

found out my old boss had given me bad references.
think maybe she did it because she was upset i left but not 100%

she was saying i did not leave on good terms & the company would not hire me back.

When i emailed the HR woman at corporate headquarters from my old job she said i did leave on good terms & i'm able to be rehired.

i wrote out my two weeks notice on feb 11th but stayed till march 19 just to help her out.

Why did she take my resignation badly?
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