Yes there is an error in schematic, probably caused by moving wires around which can cause (as it appears to have in this case) unwanted connections. The initial state of the sketch is BB has 2 connections to route (indicating an error in schematic as bb should be correctly routed now), schematic is routed and pcb has 4 nets routed (but no apparent traces which may be a problem later!). Looking at schematic the problem is pretty easy to see: several of the mega’s pins are shorted together. In most cases pins on a micro won’t connect to other pins on a micro. To fix this, in schematic view delete all the wires that connect to R27, mega pin D46 and mega pin D13. That leaves the correct connections shown by rats nest lines ready to connect again and in bb view routing is complete. This sketch has bb view partly corrected (details below) and the offending wires deleted leaving the rats nest lines:
Chewie original circuit edit_fix1.fzz (134.3 KB)
In breadboard there is a cosmetic issue: The LEDs have resistors under the LED where they can’t easily be seen (they appear to be connected correctly though). I would change the layout to make the resistors obvious (which I have done for the CLEARL and BNKL LEDs in this sketch, the other 4 need to be done the same but I was too lazy to do them 
). In this sketch the rats nest lines in schematic have been properly routed so the sketch should now be correct (although as noted 4 nets in pcb think they are already routed which may be a problem later).
Chewie original circuit edit_fix2.fzz (135.4 KB)
I would suggest that your next step in this project should be to adjust breadboard to finalize the power supply details (a 12V wall wart and a buck converter for the 5V fro the neo pixels as discussed above) so you are working on what will be (we hope anyway!) the final layout.
Peter