What do you have focused, your main or the mob you are sheeping?
What do you use to target a mob? Options [target=........], /target or /assist
Give your sheep macro and your DPS macro so we can see what is happening.

This is just my idea, I would have your alt target the mob they are going to sheep and then use target option to DPS, that way they always have the mob targeted that they will kill and can still attack the main's mob.