a. Three minutes later means "after that time".
Ann: Ben, why didn't you do what I said to you:
Ben: I forgot.
(Three minutes later Ben heard some cracks in the kitchen)
Ben: Ah... I am sorry Anna, I am doing it now for you.
b. In three minutes means "around that time not more than that."
Clark : In three minutes, I want my room clean. No more excuses. I have a very
important meeting with my clients. If you mess it, I will fire you!
Janitor: Copy that, Boss!