For anyone else who find a similar behavior of ORM Designer. The problem wasn't in traits, but inside the @Entity annotations.
There were these annotations:
* @ORM\Index(name="deletedAt_idx", columns={"deletedAt"}),
* @ORM\Index(name="createdAt_idx", columns={"createdAt"}),
* @ORM\Index(name="updatedAt_idx", columns={"updatedAt"}),
* @ORM\Index(name="uuid_idx", columns={"uuid"})
ORM Designer automatically creates all referred fields and entities, so in this case this means that ORM Designer automatically creates fields deletedAt, createdAt and updatedAt.