It seems to me that the definition of a EquivalentTo class doesn't work properly in Protégé 5.2.0. Hopefully, it is a misunderstanding on my side.
Here is the example : Link to a simple ontology that gives an unexpected result.
The problem happens when I use a min cardinality condition on some ObjectProperties. In the provided example, the classification in SubClassObject of the Object(using Pellet) doesn't work for the hasPart min 2 Part but does for hasPart min 1 Part. As you see, the element5 has 4 Parts as defined.
Has anybody ever met a similar issue?
Thank you in advance,
As @StanislavKralin said : Edit > Make all individuals different.
In my personal experience afterwards, be aware that it will considerably increase computing time of reasoning.