Using standard transparent material with albedo alpha set to 0 produces shadow artifacts when Final Gather is enabled in Enlighten bake.
Increasing Bounce Intensity on the directional light produces more visible artifacts.

Repro:

1. Open project 'TransparencyFinalGatherTest'
2. Open scene 'FinalGatherBug'
3. (If lightmap not shown, rebake the scene)
4. Observe the shadow artifacts reflected on wall behind cylinder with alpha 0 transparent material

Unity version:
5.4b18

Working correctly in:
5.3.4f1