I can confirm the same is happening here for me with Org mode version 9.4.6
(9.4.6-4-g093c94-elpa @ /home/jeff/.emacs.d/elpa/org-20210607/) on GNU
Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, cairo
version 1.16.0) of 2021-06-16
The duplicate LOGBOOK entries also seem to be messing up the graphical
display of habit records in the agenda.  Deleting the duplicates returns
the habit display to expected output.  I'd be happy to share details of
that symptom, but the root cause seems to clearly be the duplicates in the
LOGBOOK
Jeff Kowalski

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