Try to re-install libtool by:
brew reinstall libtool --universal && brew unlink libtool && brew link libtool
If that doesn’t help, try removing libtool completely, and then retry the steps above:
brew uninstall libtool
If it still doesn’t work after trying the steps above, check to see if you have the DYLD_FALLBACK_LIBRARY_PATH variable defined somewhere on the system (e.g. ~/.profile) and try unsetting it before trying the steps above again.
Other commands which could be useful for identifying the issue:
$ libtool --version
$ whereis libtool
$ set | grep DYLD_FALLBACK_LIBRARY_PATH
$ echo $DYLD_FALLBACK_LIBRARY_PATH