When using "make sure" to mean that the person is responsible for whatever follows, you can use subjunctive. "Make sure" can also mean to find out about something to and be certain about it. So, "make sure necessary measures are taken" is like telling someone, "Go see if the people over there are doing what they are supposed to and then come tell me." But "Make sure necessary measures be taken" would be like saying, "It is your responsibility to ensure that everything is done properly. If it is not, you will be accountable." You should be aware that you will not often hear the subjunctive used in this way in America. Both of the subjunctive phrases sound awkward to me (a native speaker, but also a grammar teacher!). They may be technically correct, but they are not often used. In particular, the first example about the girl being fine sounds very strange in the subjunctive. Probably because it is not typical to speak about someone being responsible for someone else's state.

It's the same as the difference between subjunctive and indicative mood.