Migrate nodes from D7 to custom entity defined in D8
It looks like you're very close. Is your entity called "phase" or "phase_entity"? If it is "phase", then you should adjust that under destination. Here is what I would recommend:

id: phases
label: Phases nodes migration
migration_group: phases    
source:
  plugin: d7_node
  node_type: phase
destination:
  plugin: entity:phase
process:
  id: nid
  type: 
    plugin: default_value
    default_value: phase
    langcode: language
  name: title
  user_id: uid
  changed: changed
  created: created
migration_dependencies: { }