Reproduction Steps:
1. Open User's project
2. Change Graphic API to GLES3
3. Set "GPU skinning" - true
4. Build to iOS or Android Device
5. Notice a lot of malfunctions/missing character's face
6. Set "GPU skinning" - false
7. Build again
8. Notice that character looks normal.

Expected: All meshes are visible and no flickering or other malfunctions.

Reproduced on: iPad Air 2 iOS 8.1, iPhone SE iOS 9.3
Reproduced in versions: Unity 5.3.4f1, 5.3.5f1, 5.3.5p4, 5.3.5p5, 5.4.0b22

Note in 5.4 editor if GPU skinning is enabled character's face is already missing.

RESOLUTION:

We disabled GPU skinning on GLES due to instability on various mobile devices and poor performance.