I've noticed a significant bug on the iPad version of Acrobat Reader, when working with the Document Cloud. If internet access is intermittent, and the app fails to sync the current document (with annotations/edits), leaving that document may fail to save those changes and update the version on the Cloud. Later, when opening the document again, sometimes the app will download the older version from the Cloud, effectively erasing all the annotations and edits done on the local file.
For me, this has resulted in hours worth of highlighting and notes being lost, as just happened. This is not a problem as long as I am consistently connected to the internet. But sometimes closing the file will result in me being unable to reopen it, as if the app automatically "purged" it from my iPad as soon as I closed it. I feel that the best behavior for the app would be to check to make sure all edits have been successfully synced before removing the file from local storage or attempting to download a version from the server.
Alternatively, there could be a warning message (similar to the desktop app) saying "the file stored on the Cloud is an older version, which one would you like to keep" would be extremely helpful.