Daily Security Run: packages missing files

[ardeaf]

Hello, first time poster but longtime user here. I recently (within the last month) started seeing this in my daily security run output. It looks like many files are missing from many different packages. The below output is just a small snippet and the actual full output stretches thousands upon thousands of lines. The pattern continues with many different packages and with each package missing a lot of files.

Code:

Checking for packages with mismatched checksums:
ap24-mod_mpm_itk-2.4.7_2: /usr/local/libexec/apache24/mod_mpm_itk.so
apache24-2.4.48: missing file /usr/local/include/apache24/ap_compat.h
apache24-2.4.48: missing file /usr/local/include/apache24/ap_config.h
apache24-2.4.48: missing file /usr/local/include/apache24/ap_config_auto.h
apache24-2.4.48: missing file /usr/local/include/apache24/ap_config_layout.h
....
binutils-2.33.1_2,1: /usr/local/x86_64-portbld-freebsd12.0/bin/readelf
binutils-2.33.1_2,1: /usr/local/x86_64-portbld-freebsd12.0/bin/strip
boost-libs-1.72.0_1: missing file /usr/local/include/boost/accumulators/accumulators.hpp
boost-libs-1.72.0_1: missing file /usr/local/include/boost/accumulators/accumulators_fwd.hpp
....
zopfli-1.0.3_1: missing file /usr/local/lib/libzopflipng.a
zopfli-1.0.3_1: /usr/local/lib/libzopflipng.so.1.0.3
zsh-5.8: /usr/local/bin/rzsh
zsh-5.8: /usr/local/bin/zsh
zsh-5.8: /usr/local/bin/zsh-5.8
....

-- End of security output --

This makes me worry, however, I am otherwise running along just fine without any apparent issues.

Is this something I should worry about? Is there a way to correct this behavior?