How many times Spring is calling single Singleton constructor?
Only once; The default Bean Scope is singleton.
In which cases constructor can be called more than one time (for bean with same id)?
Take a look at Bean Scopes
Scope Description
singleton
Scopes a single bean definition to a single object instance per Spring IoC container.
prototype
Scopes a single bean definition to any number of object instances.
request
Scopes a single bean definition to the lifecycle of a single HTTP request; that is each and every HTTP request will have its own instance of a bean created off the back of a single bean definition. Only valid in the context of a web-aware Spring ApplicationContext.
session
Scopes a single bean definition to the lifecycle of a HTTP Session. Only valid in the context of a web-aware Spring ApplicationContext.
global session
Scopes a single bean definition to the lifecycle of a global HTTP Session. Typically only valid when used in a portlet context. Only valid in the context of a web-aware Spring ApplicationContext.
What you need is scope prototype

So add a @Scope("prototype")
to your bean definition like this:
@Bean
@Scope("prototype") //add this
public MyBean myBean()
{
return new MyBean();
}