In a trial ".docx" filing of a pair of patent applications, we received several instances of the above "This document contains multiple application parts" error, flagged as a fatal error, all for the Specification part. (The Claims and Abstract sections were apparently acceptable.) Needless to say, we eventually filed both of these .pdf.
None of these errors indicated what specifically triggered this error, so what looked specific ("multiple application parts") was in reality mystery meat.
If there is a reason to render generic error information, then this should be listed as a "warning" and not as a fatal error. In the unlikely event that an application is submitted with separate Claims and Abstract documents, but also has a Specification submitted with multiple parts, this is easily resolved with a "Notice to File Corrected Application Parts" notice.
This whole experience has turned out to be an (unlabeled) beta test. For example Track 1 submissions (one of the two applications) did not even allow the ".docx" option. To demonstrate that this was not an "accidental oversight", when we went to "Nonprovisional Patent Application", we noted that "Track 1 Priority Request" was deliberately removed from the list of Nonprovisional Patent Application submissions. (Why??)
If .docx is preferred by the USPTO, why the very easily avoidable roadblocks?