""I think the first time I was just waiting to see Freida so I wasn’t really paying attention to the movie itself. But the second time is when I really enjoyed it and saw the message of the movie.‘’
It is hard to explain; I am no expert, but these sentences sound natural to me.
The first sentence is about the first time I watched this movie and the circumstances in which I watched it. You could add: “I think the first time [that I watched this movie] I was just waiting to see Freida so I wasn’t really paying attention to the movie itself.”
The progressive form “was waiting” is used to describe the thing that was happening while I watched the movie, the circumstances.
Instead of “wasn’t really paying attention” I could just as well have said: “I didn’t really pay attention”, because you could take this as the main action, or so I should think. I’d say the progressive form “was paying” is used here because the “not paying attention” is taken as a circumstance: while this “not paying attention” was happening, I watched the movie.
In the second sentence "but the second time is when I really enjoyed it and saw the message of the movie’’:
“Enjoyed” and “saw the message” are presented as the main actions that happened, they are not presented as a circumstance during which something else happened. You could rephrase it as “the second time I watched the movie, I was really enjoying it and saw the message of the movie”. Then the “enjoying” is presented as a circumstance in which “saw the message” happened, and perhaps “I watched the movie”, too. The meaning of both sentences taken together wouldn’t change much.