Piston arm appears twice during retraction in some mechanisms

The Bug

I am not sure about the exact conditions, but the piston arm consistently appears twice during the retraction phase in some mechanisms.

How to Reproduce

1. Build a simple 2-directional flying machine:
   Top view:
   
   Bottom view:
   
2. Update one of the observers
3. One of the pistons should now consistently have 2 arms during the retraction phase, such as in this screenshot: