For me, it happened when Greengenes2 plugin was installed.
...
Installing collected packages: nose, scipy, regex, msgpack, cython, nltk, scikit-bio, redbiom, q2-greengenes2
Attempting uninstall: scipy
Found existing installation: scipy 1.13.0
Uninstalling scipy-1.13.0:
Successfully uninstalled scipy-1.13.0
Attempting uninstall: scikit-bio
Found existing installation: scikit-bio 0.6.0
Uninstalling scikit-bio-0.6.0:
Successfully uninstalled scikit-bio-0.6.0
Successfully installed cython-3.0.10 msgpack-1.0.8 nltk-3.8.1 nose-1.3.7 q2-greengenes2-2024.1 redbiom-0.3.9 regex-2024.5.15 scikit-bio-0.5.9 scipy-1.10.1
Seems like installing Greengenes2 will downgrade scikit-bio and others in QIIME2-2024.5!