It seems to me that usually when the issue of internal Imperial conflicts arise, it's usually between some of the more autonomous branches (Astartes, Rogue Trader Fleets, Ministorum Cults, etc.), or between loyalists and secessionist worlds (which may or may not be chaos cultists, genestealer-infiltrated or what have you).
My question is more with regards to to sub-imperial polities (planets, systems, subsectors) that have clashed with other equivalent entities, but without either opposing the Imperium as such. Obviously clans on Feral Worlds or Feudal Worlds will exist in a state of endemic warfare, but this question is more about interplanetary warfare with a more common technological level.
Are there any good examples?