This issue is resolved in the next dot release of ArcGIS Pro (1.1).
解决办法
When a point feature layer symbolized by Unique Values is in between the hollow circle and square shape marker symbol in the Table of Contents, the layers are displayed correctly after exported to a PDF.
1. Open the attached Project Package.
2. Turn on ‘Layer1’ and ‘Layer2’.
3. Turn on layer ‘Unique_Values’, and move in between layer ‘Layer1’ and ‘Layer2’ in the Table of Contents.
4. Export to PDF. All layers are drawn correctly.
The layers are not displayed correctly if the point layer between ‘Layer1’ and ‘Layer2’ is a Single-symbol symbology.