Welcome to English in a Minute. If you arrive too late to a harbor to catch a boat, you can say you miss the boat. But as an idiom, this phrase is not about transportation. Miss the boat. Have you heard back about the pop-up book design program in Miami? Um, no. Actually, I missed the application deadline.
What? You would have loved that. You really missed the boat by not applying. If you miss the boat, you miss your chance at a good opportunity. It can also mean to not understand something. For example, you might miss the boat on an important English grammar point. Anna missed the boat. When she did not apply for a program, she would have enjoyed.