Not sure if this will help your issues, but order tends to matter with middleware. I've found for rewrite to work correctly it needed to be before status code rewrites if you use those and before Geta Not Found Handler. Here's what I've used in configure:

            using (var stream = File.OpenText("RewriteRules.config")) {
                var options = new RewriteOptions()
                    .AddIISUrlRewrite(stream);
                app.UseRewriter(options);
            }

            app.UseStatusCodePagesWithReExecute("/error/{0}");
            app.UseNotFoundHandler();
            app.UseOptimizelyNotFoundHandler();