When the artboard background is set to any non-transparent color - all generated assets (File>Generate>Image Asses) a filled with this color also the sizes (boudaries) of some exported layers are being calculated incorrect.
Here is PSD:
Steps to reproduce:
1. Ensure that File>Generate> Image Assets is turned on.
2. Look into the assets folder near psd file. There will be white square with name Test_icon.png
3. Select an Artboard in Layers panel.
4. Open Properties window and change artboard backgroung to Transparent.
5. Now exporting works correctly.