I can’t fix it because i don’t know about electronics, all i know is when i see something strange in FZ.
I see a ratsnest in BB on the Mega. I think you must have forced a connection in SCH and it thinks you now need that connection, or one of the wires in BB isn’t actually connected so FZ is putting one in.
The junctions aren’t text book, so it’s hard to know what you intended. If you look at the R27 there is a big junction on pin i but a small ones on the wires below. Big junctions signify a double or more connection, where as a small one is just a bend in the trace, and because there is on big junctions on the traces below you are never sure what is actually connected. I think I mentioned it before, but you run a trace from a part pin to a bendpoint, or you hold ALT and click on a bendpoint and make a trace to the part pin. Then grab the big junction and move it around and check all the traces stay connected and move with it - 4 junctions are a bit weird and don’t all move -.
Other rules is that you always have a black trace between parts, ie no part pin to part pin, and no part pins sitting on traces, eg R28. This like that can lead to thinking you have a connection when you don’t.
Other than those fine points it looks pretty neat.
If you want to switch to other EDAs they don’t have a BB view, which is one less headache to worry about, and they force you to do the whole SCH first and export it into PCB view, which has less chance of errors, if the SCH is correct, because the views aren’t connected.