I am considering moving up a division after having only been in DIII for one season. When looking at potential jobs I got a message that said I could do better than an A+ prestige DII school. How is that possible? Yet I was told I would be a good fit for a B school at DII.

If you had any sort of decent season at DIII, you should be eligible for any DII job you like.  If you like the A+ school and its returning roster, then apply for it.  

Be warned: make sure you compare returning rosters and the conference to choose the best spot.  Normally the A+ prestige school will have the better returning roster, but certainly not always.

I am qualified for both jobs. I just thought it was odd that they said The A+ school was not as prestigious according to the comment