Let’s say I decide I’ve had enough with this whole Federation business and that humanity would be better represented by a Starfleet that follows my particular ideology. Assuming I could get enough people for crew and support, why can’t I start my own Starfleet?
I could replicate ship parts until I have a couple vessels. Go to new worlds and present myself as the official first contact of humanity. I could fly to Vulcan or Bajor and tell them no actually my organization represents humanity.
What’s going to stop me?
The Laws of Thermodynamics say you will always lose some energy to heat when energy is used to affect a change. I have to imagine this would be particularly so when energy is converted to matter since that’s very involved, but I’m not a physicist so I can’t confirm that.
Come to think of it, this means that industrial replication plants and shipyards would likely be incredibly hot places, due to the inevitable loss to heat in replicating massive components.