I have Atlas, with required and optional dependencies in mods folder.

I do not have the either know incompatible mods in the folder.

When I try to open MC with current list of mods, it crashes and I get "Exit Code:1"
If I load just Atlas maps and Moonlight Lib, it works fine.

Has anyone else experienced a similar problem?

Send latest.log

And never install mods manually, that's rookie mistake. Use a launcher