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This is a bug we have found and fixed. Can only happen if you save your project while the autosave is running. Thanks for reporting.
However, there is also no need to save a document or a project manually at all. Documents and Projects get saved every few seconds automatically. The reason to save a document is to overwrite the closed version. BTW: We will drop the "save project" command completely in the next upcoming release of Ulysses. It's just not needed.