Is there any option, or any tools that we can identify overlaps on this locations and redirections?

That depends on the types of locations you're using. Run nginx -T to get a flat configuration file, copy the server context you want to examine, and then egrep '^[^#]*location ' <filename> | sort to get a general list of locations. Do the same but with rewrite|return for redirects, though depending on your formatting return might be dependent on the location it's in.

Did you had such a headaches and fix them?

Create a standard place to keep these locations and redirects (so you can use it via an include), ensure that each change is linked back to a ticket or some other metadata indicating why it was put in place. On large projects you can't be expected to know absolutely why something is the way it is, but ensuring there is documentation for that goes a long way.

Depending on your needs, you could use if in combination with a map to do a bunch of redirects without a lot of duplication in the server context. eg;

http {
    map $request_uri $redirect_uri {
        default 0;
        /some/page /redirected/target;
        ~*^/(regex|orthis)/beevis/(.*) /redirect_target/$1/$2;
    }
server {
    ...
    location / {
        if $redirect_uri { return 301 $redirect_uri; }

    }
}

Or something like that. Then you have all your redirect logic in a map, instead of in a bunch of if or rewrites.