On Tuesday 12th Nov, Dokku4 ran out of disk space. This prevented us from doing new deployments and could have caused further issues too.
Running dokku cleanup didn't free up any additional space. However, running docker system prune did delete a large number of build cache objects and freed up 132G of space. Taking disk usage down from 100% to 17%.
It appears that there's a known issue with Dokku failing to clean up appropriately when deploying via git:from-image. This may or may not have caused the problem.
Until Dokku release a fix, or unless we find a workaround, we should regularly run docker system prune.