This may be a Cryptomator limitation.
This Message has nothing to do with free space problems. It indicates that a file request/operation took more than 10s to be started and therefore was aborted. Dokany uses 5 worker threads to handle requests. If noew every single of them is busy, another request comes in and the threads stay busy for the next 10s this request will be dropped. Unfortunatley Dokany does not allow a dynamic worker thread pool.
When issue #802 is implemeted, the user can set the number of threads by himself.