Is there anyway to track down what is filling up /overlay? I am using Banana Pi R64 which, only seems to have the squashfs. Also, the packages that I have installed (including dependencies) only fill 80% of /overlay when I got the setup working as I wanted. However, now something is filling up the rest of the space and I can not figure out what it might be.
If trendy's command doesn't yield the culprit and your system keeps the real time clock fairly accurate shortly after each boot then try listing files with dates and see what is newer than "when I got the setup working as I wanted".
ls -ltrR /overlay/
(The -tr switch to ls sorts by modification time with newes at the bottom.)