[2015-10-03 22:10:53.948377] TransferScanner: warning TransferScanner crashed: unknown response from git cat-file ("refs/heads/git-annex:706/2a9/SHA256E-s13840914--38cdcf384aee777000693f58f1302684bf18f577045c1340d7aeb72b6d6f2233.dmg.log.cnk missing","refs/heads/git-annex:b8f/4d2/SHA256E-s26301635--ce2f215486df83c6ada74a81679ff78f717404d0637bfd51ecbf0330c21db12b.dmg.log")
What exactly is this telling me?

This message suggests that your git repository has somehow lost an object that was committed to it. Suggest you run
git annex repairto fix whatever the problem might be.