Why did Experiment One not get a counter when my Undying creature returned to play?
Well, it should have.

In the ruling for Experiment One it clearly stats: 
If a creature enters the battlefield with +1/+1 counters on it, consider those counters when determining if evolve will trigger. For example, a 1/1 creature that enters the battlefield with two +1/+1 counters on it will cause the evolve ability of a 2/2 creature to trigger. 

You should report this bug to the MTGO support.