When you recover from some physical or emotional state, you get over it. Example: "I was very sick yesterday, but I have gotten over it."

When something is bothering you, it is like an obstacle that is in your way, and you need to get over it. Example: "How are things with Jane?" Reply: "Actually we broke up last month. But I have already gotten over it."

You get over something when you are no longer affected by it. Example: "I just can't stop thinking about what she said." Reply: "Don't worry, you'll get over it." Another example: "Oh, just get over it."