Every ghostwriting client I've ever had does two things. These aren't really mistakes, they do show their excitement and commitment to be an author of their story, but these two things always need to be set aside at some point.
The first is the book's title. Everyone has a title they want and often these are relatively good. The second is they have a cover they want to use. Again these are often relatively good.
However, the first thing an agent and/or publisher is going to want to do is change both.
This fact cuts to the main point of this post: publishing is a business and when you sign on with an agent and then a publisher they have a level of experience with marketing books that you don't have. They understand, for example, how certain colors send subtle signals to readers (light blue for redemptive books). They understand how a title can influence a potential reader to pull the book from the shelf and begin the process of deciding if they want to pay money for it.
Let your agent and publisher have a say in your cover design and title. It doesn't mean roll over--if they make a mistake, tell them what you think--but you do need to allow them to do what they do best, market books. After all, they want your book to succeed as much as you do. They are investing considerable sums to produce, publish and distribute it and they want to recoup those costs and make a tidy profit.