science/openbabel has USES+=python in its Makefile, which will normally pull in lang/python and from there lang/python27, properly recording this dependency. However, if lang/python34 is also installed, one of the files installed by openbabel will be linked against a library installed by python34:

# ldd /usr/local/lib/python2.7/site-packages/_openbabel.so
/usr/local/lib/python2.7/site-packages/_openbabel.so:
        libpython3.4m.so.1 => not found (0)
        libopenbabel.so.4 => /usr/local/lib/libopenbabel.so.4 (0x8018df000)
        libm.so.5 => /lib/libm.so.5 (0x801d10000)
        libz.so.6 => /lib/libz.so.6 (0x801f38000)
        libc++.so.1 => /usr/lib/libc++.so.1 (0x80214e000)
        libcxxrt.so.1 => /lib/libcxxrt.so.1 (0x80240e000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x80262a000)
        libc.so.7 => /lib/libc.so.7 (0x80081f000)
# : (on another machine)
# pkg which /usr/local/lib/libpython3.4m.so.1
/usr/local/lib/libpython3.4m.so.1 was installed by package python34-3.4.3_1
#

This is clearly wrong (/usr/local/lib/python2.7 should not contain files referencing another python installation), and this dependency is not recorded.