This is not an issue and doesn't need to be turned into one. I can see why the kid said what he said. I can see why the coach said what he said. It was a heat of the moment thing and can be easily overcome unless people are super sensitive. I do believe the catcher needs to talk to the coach to understand exactly what he wants in terms of leadership. Here's the problem I see - how many coach talk about leadership? Every single one of them. But how many actually TEACH leadership? Rarely does it happen and that's the crux of the problem. We tell kids to lead but they never have so how do we expect them to be successful if we don't provide the structure to know how to lead?
Overall as a coach I don't have a problem with what the catcher said except the "It's OK" part. Well it's not OK because a mistake was made that hurt the team. So we don't need to justify or validate the mistake by saying it's OK. I'm a big believer in saying "shake it off" or "relax let's refocus" or something like that. A mistake was made that put us in the hole. It's never going to be OK but we do need to get back in the game. The game won't stop so we can talk about our feelings so we need to shake the mistake off because we can't let one mistake turn into more. Anyway, that's my feelings on what should / should not be said.
Side note about the catcher saying "calm down" - nothing cracks me up more than the person saying calm down in a super excited way. Not sure if I can truly describe it over text but it comes out as "CALM DOWN.....JUST EVERYONE CALM DOWN" How can people calm down if you're not calm yourself?
As for the cut situation I agree the RF should be able to get the throw to 3B but you still need someone for an off line throw or to go after a runner at 2B. We use the SS as the cut / relay man to all OF throws to 3B. The SS has the less area to cover to get in that position versus the 2B.