angular-cli: Universal --bundle-dependencies=all works with --aot but fails with --prod

Versions

Angular CLI: 1.6.0
Node: 8.9.1
OS: win32 x64
Angular: 5.1.0
... animations, common, compiler, compiler-cli, core, forms
... http, language-service, platform-browser
... platform-browser-dynamic, platform-server, router

@angular/cdk: 5.0.1
@angular/cli: 1.6.0
@angular/flex-layout: 2.0.0-beta.11-b01c2d7
@angular/material: 5.0.1
@angular-devkit/build-optimizer: 0.0.35
@angular-devkit/core: 0.0.22
@angular-devkit/schematics: 0.0.40
@ngtools/json-schema: 1.1.0
@ngtools/webpack: 1.9.0
@schematics/angular: 0.1.10
@schematics/schematics: 0.0.10
typescript: 2.4.2
webpack: 3.10.0

Repro steps

When using below command it works perfectly.

ng build -- --app=ssr --output-hashing=media --aot --bundle-dependencies=all

But when we run below command:

ng build -- --app=ssr --output-hashing=media --prod --bundle-dependencies=all

It throws below warnings:

WARNING in ./node_modules/@angular/core/bundles/core.umd.js
6579:23-44 Critical dependency: the request of a dependency is an expression
    at ImportLazyContextDependency.getWarnings (D:\MyProject\ClientApp\node_modules\webpack\lib\dependencies\ContextDependency.js:39:18)
    at Compilation.reportDependencyErrorsAndWarnings (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:703:24)
    at Compilation.finish (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:561:9)
    at applyPluginsParallel.err (D:\MyProject\ClientApp\node_modules\webpack\lib\Compiler.js:502:17)
    at D:\MyProject\ClientApp\node_modules\tapable\lib\Tapable.js:289:11
    at _addModuleChain (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:507:11)
    at processModuleDependencies.err (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:477:14)
    at _combinedTickCallback (internal/process/next_tick.js:131:7)
    at process._tickCallback (internal/process/next_tick.js:180:9)
 @ ./node_modules/@angular/core/bundles/core.umd.js
 @ ./src/main.server.ts
 @ multi ./src/main.server.ts

WARNING in ./node_modules/@angular/core/bundles/core.umd.js
6599:23-110 Critical dependency: the request of a dependency is an expression
    at ImportLazyContextDependency.getWarnings (D:\MyProject\ClientApp\node_modules\webpack\lib\dependencies\ContextDependency.js:39:18)
    at Compilation.reportDependencyErrorsAndWarnings (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:703:24)
    at Compilation.finish (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:561:9)
    at applyPluginsParallel.err (D:\MyProject\ClientApp\node_modules\webpack\lib\Compiler.js:502:17)
    at D:\MyProject\ClientApp\node_modules\tapable\lib\Tapable.js:289:11
    at _addModuleChain (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:507:11)
    at processModuleDependencies.err (D:\MyProject\ClientApp\node_modules\webpack\lib\Compilation.js:477:14)
    at _combinedTickCallback (internal/process/next_tick.js:131:7)
    at process._tickCallback (internal/process/next_tick.js:180:9)
 @ ./node_modules/@angular/core/bundles/core.umd.js
 @ ./src/main.server.ts
 @ multi ./src/main.server.ts

And when we run the app it shows below error in log:

 StaticInjectorError[InjectionToken DocumentToken]: 
  StaticInjectorError[InjectionToken DocumentToken]: 
    Right-hand side of 'instanceof' is not an object