The behavior can be reproduced only when Flange is created on the edge created by Face and then you move EOP to above Flange1 to create Thicken. "Automatic Blending" option in Thicken command actually makes Thicken behave more like Move Face. You can reproduce the same behavior by swapping Thicken/auto blend to Move Face. And, you will get the same result.
The edge creating Flange was created by Face, not Thicken. Thicken simply "moves" the edge farther. Did you notice that even when Thicken is suppressed, Flange can still compute?
The behavior is indeed confusing. I will follow up with development and see what can be done with it. In the meantime, you could either create zero-angle Flange or Thicken/auto blend off for this case to avoid the behavior.
Many thanks for letting us know!