Professor submitted my letter of recommendation after I removed him I had sent a reminder to the professor for submitting my letter of recommendation about two days before the deadline, but he didn't reply to me. He was highly unresponsive after initially agreeing. As the deadline was approaching, I removed him from the recommender list, thinking that he might be too busy to write the letter. But he submitted the letter a few hours before the deadline, and emailed me that the system didn't accept his letter.
It's so embarrassing. I am not sure how I should reply to him. It makes it look like I don't believe him but I did believe it made sense to change the recommender at that moment.
Your perception was entirely reasonable, and as somebody who is serious, you can't let unreliable people decide your fate. So, it is very logical, and nobody should blame you because you did the best thing you could. The point is, should you even communicate the substitution to him, and if yes, what good does it do? If you couldn't find any reason for doing so, then perhaps you shouldn't. This whole recommendation letter is entirely about you and given that he didn't even bother to check or post, you can just simply ignore him. A few months later things will be back to normal and people will simply forget about it.