Never mind!
I figured out what was wrong!
Thank you for your help!
And PLEASE let me know if there are any other bugs.
There is one more thing I almost forgot to mention; when clearing out the dock I messed up and escaped from the last battle but that caused the game to stop progressing despite the fact I was able to play like normal. Because of that I had to start over but it was mostly my fault for the mistake even if it was unintentional. Maybe disabling the escape option from fights I can't avoid to prevent this from happening might help but I'll leave it up to you. That and I need to work on explaining things with less words, sorry. ^^;;