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