I a trying to generate an HTML coverage report, but it does not contain the output I expect. Maybe I'm wrong here, but it should show only those lines and methods covered which are called from the spec file, right?

Somehow it does not.

Update:

I created an repository to provide a working example, outlining the problem:

https://github.com/gearsdigital/stunning-octo-train

This is my (test) project setup. I'm able to push it to a GitHub repo if needed as I don't know how to setup JSFiddle to run this code.

TL;DR

There is a process to generate an HTML coverage report. This report shows code as covered which is obviously not covered because there is no test available.

karma.conf.js:

var webpack = require('webpack');
var path = require('path');

// Reference webpack.config.js, don't repeat it!
var webpackConfig = require('./webpack.config.js');

// The entry point from the referenced Webpack configuration has to be
// removed or tests will fail in weird and inscrutable ways.
// Easy enough, just define an empty entry object (null won't work).
webpackConfig.entry = {};
webpackConfig.module = {
    preLoaders: [
        {
            test: /\.js$/,
            // files within these directories should be excluded
            // for babel processing
            exclude: /(node_modules)/,
            loaders: ['babel?cacheDirectory']
        },
        {
            test: /\.js$/,
            include: /(src\/js)/,
            exclude: /(vendor)/,
            loaders: ['isparta']
        }
    ]
};

/**
 * Karma configuration
 * @param config
 */
module.exports = function (config) {
    config.set({
        browsers: ['PhantomJS'],
        coverageReporter: {
            dir: 'test-results',
            reporters: [
                {type: 'text-summary'},
                {type: 'html', subdir: 'coverage'}
            ]
        },
        files: [
            'webpack.test.config.js'
        ],
        frameworks: [
            'jasmine'
        ],
        preprocessors: {
            'webpack.test.config.js': ['webpack']
        },
        reporters: ['spec', 'coverage'],
        webpack: webpackConfig
    });
};

webpack.config.js:

var webpack = require('webpack');
var path = require('path');

module.exports = {
    plugins: [
        new webpack.ProvidePlugin({
            $: "jquery",
            jQuery: "jquery",
            "window.jQuery": "jquery"
        })
    ]
};

webpack.test.config.js:

// make sure the file name regexp matches your test files.
var testsContext = require.context('./tests', true, /\.spec\.js$/);
testsContext.keys().forEach(testsContext);

// make sure the file name regexp matches your test files.
var srcContext = require.context('./src/js', true, /\.js$/);
srcContext.keys().forEach(srcContext);

bootstrap.js:

import {Calculator} from './modules/Calculator';
let c = new Calculator();
c.add(1,2); // 3

Calculator.js:

export class Calculator {
    add(op1, op2) {
        return op1 + op2;
    }

    sub(op1, op2) {
        if (typeof op1 !== 'number') {
            return false;
        }
        return op1 - op2;
    }

    mul(op1, op2) {
        return op1 * op2;
    }

    div(op1, op2) {
        return op1 / op2;
    }
}

bootstrap.spec.js:

import {Calculator} from '../src/js/modules/Calculator';

describe('Calculator', function () {

    it('should return 10', function () {
        expect(true).toBe(false);
    });

});

Generated report:

I expect add() to be uncovered, as it's not called in any test but in bootstrap.js.

Project structure:

src/js/bootstrap.js gets loaded; which means these lines get executed.

import {Calculator} from './modules/Calculator';
let c = new Calculator();
c.add(1,2); // 3

I am guessing this block is the culprit:

    {
        test: /\.js$/,
        include: /(src\/js)/,
        exclude: /(vendor)/,
        loaders: ['isparta']
    }

Shouldn't my code be only exercised during tests?

The short answer is no.

Anything that is not located inside closures / function / methods may get covered when you import the module.

// this will get coverage; because it is top-level code outside a function block
var dummy = null;

export class Calculator {
    add(op1, op2) {
        // this will get coverage only if you call explicitly the function.
        return op1 + op2;
    }
}

// this will get coverage.
var c = new Calculator();
// and now, Calculator.add will get coverage.
c.add(1,2); // 3