Hmmm, in Atom, my find and replace highlights all of them, and you can choose to bounce back and forth between them. It sounds like your project is kinda big.
I would suspect that’s happening in some compiled code that’s had it’s debugging information stripped. Your Lua code would generate files and line numbers. I suspect it’s probably a plugin that’s getting a nil value passed to it when it’s expecting a number.
It could be in our core somewhere, but we are pretty good about keeping out stack traces around until you actually build. Have you added or changed calls to a plugin around the time this started happening?
Rob
I didn’t see Robs reply, but he’s right on the money.
It wasn’t a ‘new’ plugin, but more an untested piece of code. It was the Dynamic shader that was causing the failure. (Since I rewrote a lot of the code, I was appalled to see the error back. BUT it was immediately as I added the shader 
So, problem solved, and shader objects destroyed.
So, short answer - these kinds of errors might well come from a plugin you are using.