Have you ever been to Japan?

Tom has gone to Japan.  =   he went to Japan
Tom has been in Japan.   =   he didn't come back
Tom has been to Japan.   
                                                                  =    he visited (and left) Japan

 
This expression is used when 

the person is not in that place anymore



BUT, please,


 GIVE SOME ATTENTION TO THESE CASES                                             

 "Have been" ( generally + TO or IN ) has the sense of "visit a place and come back."

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"I've been IN the hospital"      =    I've BEEN A PATIENT in the hospital."I've been TO the hospital"    =    I've VISITED the hospital;
 _______________________________________________________________________ 

"I've been IN a lot of trouble"    =    I've been FACING PROBLEMS


"I've been TO a lot of trouble"    =    I've been MAKING a lot of EFFORT


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sources:
pearsonlongman.com