Seems like A LOT of stuff is being talked out. I think Leonardo is aware that that mark on Michelangelo's collarbone is indeed a "bite" mark. Knowing Leo's character, almost nothing escapes his sharp ninja eyes.
Given the conversation they had, I know Mikey was trying to get Leo's attention "away from" the bite mark. No such luck. Once Leo's focused on something, he's on it.
I don't know what happened in any previous Chapters of this story, but I rarely ever hear about Mikey being angry. Most of the time Michelangelo's very nice and loves to mess around. I sure love that about his personality; but to be angry... that's a rare thing. Mostly when he's up against really horrible people.
The way I see it, whatever Leo was telling Mikey about Raphael, I think Leonardo is trying to protect Mikey. I've seen it before with Raph about his anger. Raph does have some "demons". Personal demons. His temper isn't the only thing; there is more going on with Raphael.
What Leonardo also said about "secrets" is also true. I remember how Splinter didn't tell his sons about Shredder, but he finally did when Leo made his first encounter with Oroku Saki.  Secrets will get you killed.