I have seen that occasionally as well.
If you reselect a highlight again, you should get "Remove highlight" and "Add note". But, if you adjust the highlight (grab the handles and move them), you should get the "Save highlight" option to save the change.
My guess is that there is a circumstance where it calculates the selected text and gets it wrong for comparison to the original. I think that is most likely to occur for multi-word selections or of it goes across tags. I haven't paid enough attention to this to come up with a pattern.
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