Tense Agreement

My mother said to us, ''What were you doing yesterday?''  

My mother asked us, "What we were doing the previous day?"

Or, 

my mother asked us, "What we had been doing the previous day?".

Which one is correct??

There is no difference between "yesterday" and "previous day" and they can be used interchangeably in all three of your examples. 

My mother asked, "what were you doing yesterday?" 

My mother asked us what we were doing yesterday. 

My mother asked us what we had been doing yesterday. 

All of these are correct.