Copied a Filter Miniloader that had a red wire and another Miniloader with green wire. and it resulted in this.
Error while running event fiber-optics::on_player_setup_blueprint (ID 70)
fiber-optics/scripts/blueprint.lua:115: assertion failed!
stack traceback:
[C]: in function 'assert'
fiber-optics/scripts/blueprint.lua:115: in function 'save_to_blueprint'
fiber-optics/scripts/blueprint.lua:158: in function 'setupBlueprint'
fiber-optics/scripts/event-setup.lua:158: in function 'handler'
stdlib/stdlib/event/event.lua:342: in function 'pcall'
stdlib/stdlib/event/event.lua:362: in function 'dispatch_event'
stdlib/stdlib/event/event.lua:438: in function <stdlib/stdlib/event/event.lua:396>
4702.844 Error ServerMultiplayerManager.cpp:92: MultiplayerManager failed: "The mod Fiber Optics (0.0.2) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event fiber-optics::on_player_setup_blueprint (ID 70)
fiber-optics/scripts/blueprint.lua:115: assertion failed!
stack traceback:
[C]: in function 'assert'
fiber-optics/scripts/blueprint.lua:115: in function 'save_to_blueprint'
fiber-optics/scripts/blueprint.lua:158: in function 'setupBlueprint'
fiber-optics/scripts/event-setup.lua:158: in function 'handler'
stdlib/stdlib/event/event.lua:342: in function 'pcall'
stdlib/stdlib/event/event.lua:362: in function 'dispatch_event'
stdlib/stdlib/event/event.lua:438: in function <stdlib/stdlib/event/event.lua:396>"
4702.844 Info ServerMultiplayerManager.cpp:816: updateTick(16893283) changing state from(InGame) to(Failed)
4702.845 Quitting: multiplayer error.

Copied a Filter Miniloader that had a red wire and another Miniloader with green wire. and it resulted in this. It does not crash when it is a ghost.
Error while running event fiber-optics::on_player_setup_blueprint (ID 70)
fiber-optics/scripts/blueprint.lua:115: assertion failed!
stack traceback:
[C]: in function 'assert'
fiber-optics/scripts/blueprint.lua:115: in function 'save_to_blueprint'
fiber-optics/scripts/blueprint.lua:158: in function 'setupBlueprint'
fiber-optics/scripts/event-setup.lua:158: in function 'handler'
stdlib/stdlib/event/event.lua:342: in function 'pcall'
stdlib/stdlib/event/event.lua:362: in function 'dispatch_event'
stdlib/stdlib/event/event.lua:438: in function <stdlib/stdlib/event/event.lua:396>
4702.844 Error ServerMultiplayerManager.cpp:92: MultiplayerManager failed: "The mod Fiber Optics (0.0.2) caused a non-recoverable error.
Please report this error to the mod author.

Error while running event fiber-optics::on_player_setup_blueprint (ID 70)
fiber-optics/scripts/blueprint.lua:115: assertion failed!
stack traceback:
[C]: in function 'assert'
fiber-optics/scripts/blueprint.lua:115: in function 'save_to_blueprint'
fiber-optics/scripts/blueprint.lua:158: in function 'setupBlueprint'
fiber-optics/scripts/event-setup.lua:158: in function 'handler'
stdlib/stdlib/event/event.lua:342: in function 'pcall'
stdlib/stdlib/event/event.lua:362: in function 'dispatch_event'
stdlib/stdlib/event/event.lua:438: in function <stdlib/stdlib/event/event.lua:396>"
4702.844 Info ServerMultiplayerManager.cpp:816: updateTick(16893283) changing state from(InGame) to(Failed)
4702.845 Quitting: multiplayer error.

Thanks for reporting this! This is a weird issue. It means that there are two entities with the exact same coordinates and names present in the blueprint. I tried with a miniloader and could not reproduce it. I changed the code in the upcoming 0.1.0 release to no longer throw an assert but ignore the second entity with the same coordinates (the code should also only care about the internal entities, not everything in the blueprint).