A major mistake on a metal roof

In this picture, you can see that the transition metal makes a downward swoop as it goes under the upper metal. This creates a dam where the water is filling up under the metal, going up the roof, and over the transition metal. This is how the water is getting under the metal and causing it to leak

Under this section of roofing, there should be closures. They are foam inserts that keep wind-blown rain, bugs, and small animals. Here are examples of what they look like and where they go.