When my little one and I have an argument or disagreement, yes, his "sub-ness" can hinder him from expressing himself. But in those moments, when our relationship is "less than peachy", that is when I shut the hell up and listen the most. If I go into Dom mode at all, it is to force him to talk, because I need to know what's going on.
Because whatever is going on in both of our minds and both of our hearts has to come to the table, so we can discuss it, and resolve it. I would never, ever, ever try to oppress his real feelings and thoughts about something that was making him upset. I do the opposite; I encourage him with whatever I have to talk. I assure him that all bets are off, he can tell me what he's really feeling without fear of retribution, even if he knows I won't like what he's going to say. My goal is for our relationship to last, and that can only happen if we deal with issues as they arise.
Ignoring something or just trying to shut him up will not be useful, since he will still have such feelings and thoughts, and then they'll just brood.
So when we argue, who is "right" or "wrong" is less important than that we both feel our partner heard our side, cares about our point of view, and loves us enough to want to fix it.
I have apologized for things my share of times, and so has he. Most arguments end with both of us apologizing for saying something we didn't mean. We're both human, so of course we both have moments where we hurt each other. But so long as we both believe we'd never want to hurt the other, and that we sincerely wish to correct the situation, we can remind each other that our love is stronger than some argument and we'll get through it, solve it, and be happy again.
Oh, and make-up sex is definitely the best kind of sex you can have; because that is when you appreciate each other's company the most.