Others can probably answer this better than me, but here is what I have run into.
1) Log files eating up all of the room. Several threads have talked about this. When I run into this I usually do something like:
rm -r /etc/log/journal/*
2) I have run into this a few times (latest was today). I setup the machine, I setup to to Alext's repos, I also setup to be able to upgrade my MRAA installs, and do something like:
opkg update
opkg uprade
The upgrade will upgrade lots of stuff, including maybe kernel. This is where I ran out of space today. There have been a few threads talking about the fact that the boot partition is not created to it's full size, which can cause these issues. I followed AlexT's instructions on how to resize the partition that is part of his bllog How to install a kernel from my repo onto Edison with the official image
Hope that helps