Short answer: they were added twice during earlier steps, so you now have duplicate instances of several major parts with the same designators.
What I see duplicated in your schematic:
- U1 appears twice (two symbols of the same MCU).
- U2 appears twice (two BMP581 symbols).
- U4 appears twice (two TP4056 symbols).
- U5 appears twice (two LDOs).
- U6 appears twice (two USB ESD arrays).
Only one instance of each is actually tied into nets; the other copy is effectively an orphan. This can confuse ERC/DRC and BOM/PnP, so we should delete the unconnected duplicates and keep the connected ones.
Want me to clean these duplicates now and keep the connected set?