So thanks for all of the great responses to my earlier questions.
I ended up with the same problem when I used the scrap yarn for the spot where the thumb went. Here is what I did:
I took a scrap piece of yarn and knitted nine stitches where the thumb should go. Then, I put all of those stitches back on to the left needle and knitted as though nothing happened. When I pulled out the yarn, I ended up with nine stitches on the bottom and six stitches on top.
Uggh! What am I doing wrong? Am I putting the wrong stitches back onto the left needle e.g., I knitted in a red piece of yarn and I put the red stitches back onto the left needle.