"point out" means "refer to something that the listener already knows." EX: When Sally asked for ice cream for dessert, her dad pointed out that she'd already eaten a candybar, and suggested that she eat fruit instead. Sally already knows that she'd eaten candy, so her dad "points it out". "Pointing out" is very similar to "reminding". "Indicate" is just used to report speech indirectly. EX: When Sally asked if she could go swimming, her dad indicated that she could.

There is a subtle difference and I wouldn't worry about it as a novice learner. "Indicate" is more common. "Point out" is informal.