Doesn't happen for me, but then I might not have the right data.
CC uses the series sort value that comes from calibre, controlled by the tweak save_template_title_series_sorting. If the tweak is not 'strictly_alphabetic' then calibre uses the title_sort rules for the series. My guess is that you have changed the title sort rules so that "the" and "and" are significant no matter where they appear in the series (or title). Could you check that?
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