Generally speaking, when parties share custody of their children they share joint decsision making as well.  You need to make sure that is what your agreement states.  And if that is the case she needs to consult you.  However, if it is a situation such as an emergency situation (which it can be) then she may be able to take them as needed and in their best interests.  Speak with her.  It is better to approach this in a diplomatic and pleasant way.  Good luck.