I got a funny little envelope from the mail carrier saying I owe $3.01

Since I haven't mailed anything from my mailbox, I called the local post office to find out what it was for, and he said it was most likely for something sent to me.  Hmm... I have a book on the way to  me that is coming past due so I suspect that it didn't have postage on it.  $3 isn't the end of the world, but since I already spent a credit on it, I am not too excited to pay twice so to speak.  How should this be handled?

Help documents have some guidelines for this situation Sheryl  

Basically, you can refuse the book and let the sender deal with it (return postage is not included in Media Mail prices).  This is the method recommended by PBS.  The book will eventually go lost and your credit will be refunded.

Or you could pm the member you suspect the package is from, and politely inquire as to whether or not it's possible they forgot to add postage.  If so, they might refund your credit and you can go ahead and pay the amount due and pick up the book. 

bet you the sender tried to send it media mail but used prioty box  

There's several possibilities.  The 'suggested postage' box on PBS labels can look like printed postage.  I've had counter staff try to toss my books into the sorting bins before adding postage...I'm like "no, no, those need postage first!"

If you refuse the book then you never have to mark it as received.  You will get your credit back when it goes lost in the mail so you're not out a credit for the book yet.