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.