Mine has nothing to do with minecarts, it's specifically testing for any player within a three block radius of the command block and I get the same output error.
My command is a simple: testfor @p[r=3], the error I get is [timestamp] /testfor is only usable by commandblocks with analog output.
This same command was working fine in the previous snapshot.
@Ethan Brown, if you have access to the server you're using (and I'm assuming you do since you're using a snapshot), you can just revert to the previous snapshot (13w38c I believe), and your command blocks will work again, at least it did for me.
I'm sure they'll work out the error in the new snapshot in short order.