Would not God giving people a Commandment not to kill, but then commanding people to kill others, even innocents, be considered a contradiction?

I have been thinking lately how odd it is for God to give a Commandment to not kill, but then demand his followers to slay both animals and people, innocents even. It did not have any exceptions like "Thou shall not kill unless commanded to by me to.", just "Thou shall not kill". So I feel this is contradiction. Is this correct?