If you animate undead, the generated undead is classified as a murderer, even if the animator is of blue notoriety. In Trammel, attempts to damage the target result in "you cannot perform negative acts on your target". This is problematic at least in EC, since macros that target enemies will erroneously target this, and then fail. Note that in FEL, you can happily target these. Perhaps these should inherit the notoriety of the animate undead caster?
You cannot use the necromancy "command undead" mastery to turn around and take full control of the newly animated undead. This seems inconsistent, as indeed, the being is classified as undead.