Things go in all directions, away from the speaker; things come from all directions, towards the speaker. The children ran in all directions = They ran away from you, all going to different places. The children ran from all directions = They ran towards you, all coming from different places.

They have completely opposite meaning

But our teacher told me that sometimes their meanings are the same.Is it right?

In all directions = something is going out from one spot. Think of the sun sending light in all directions. From all directions = there is stuff coming to one spot from everywhere. Think of a balloon going under water. It is being compressed from all directions.