How can we just apply the updates to a single module using composer without apply patches for other modules? We have the following composer.json file. When we want to update a module such as  Environment Indicator, we run the suggested composer command composer require drupal/environment_indicator:^3.7'. 

In doing so it also applies the patches for core and other modules because the patches is defined in our composer.json file. 

What we tried this as well but it had the same results. 

composer update drupal/environment_indicator --with-dependencies

composer.json

{
    "name": "drupal/drupal",
    "description": "Drupal is an open source content management platform powering millions of websites and applications.",
    "type": "project",
    "license": "GPL-2.0-or-later",
    "require": {
        "composer/installers": "^1.0.24",
        "drupal/core" : "^8.6",
        "wikimedia/composer-merge-plugin": "^1.4"
    },
    "minimum-stability": "dev",
    "prefer-stable": true,
    "config": {
        "preferred-install": "dist",
        "autoloader-suffix": "Drupal8"
    },
    "extra": {
        "_readme": [
            "By default Drupal loads the autoloader from ./vendor/autoload.php.",
            "To change the autoloader you can edit ./autoload.php.",
            "This file specifies the packages.drupal.org repository.",
            "You can read more about this composer repository at:",
            "https://www.drupal.org/node/2718229"
        ],
        "merge-plugin": {
            "include": [
                "core/composer.json"
            ],
            "recurse": true,
            "replace": false,
            "merge-extra": false
        },
        "installer-paths": {
            "core": ["type:drupal-core"],
            "modules/contrib/{$name}": ["type:drupal-module"],
            "profiles/contrib/{$name}": ["type:drupal-profile"],
            "themes/contrib/{$name}": ["type:drupal-theme"],
            "drush/contrib/{$name}": ["type:drupal-drush"],
            "modules/custom/{$name}": ["type:drupal-custom-module"],
            "themes/custom/{$name}": ["type:drupal-custom-theme"]
        },
        "enable-patching": true,
        "patches" : {
            "drupal/core": {
               "issuenumber1" : "path/to/patch.patch",
             }, 
            "drupal/eck": {
               "issuenumber2" : "path/to/patch.patch",
             },
        }
    },
}
Unfortunately, composer is always going to apply any patches you have defined that are not already applied whenever it runs. You can comment out the patches, run your composer command, and then uncomment them.