I had the same problem, there's definitely something wrong with the installer (I was trying to set up 14.04 with encrypted partitions on different drives, with / on my small SSD and /home /usr /tmp /var and swap on my HDD). But I played around with it, restarted the installer/rebooted a number of times, and here's how you work around it:
Set up all your actual partitions, including your encrypted containers. I believe it necessary to include an encrypted partition for swap, so make sure to make one of suitable size for it.
Once you have them all set up, THEN, and only then pin them to actual mount points. I started with swap and then moved on to /home and so on.