our client just had the same issue when he try to confirm the SO.
this is the reason why this error is happening:
_sql_constraints = [ ('name_uniq', 'unique(name, company_id)', 'Reference must be unique per company!'),]
this is a sql constrain in the "stock.picking" model, from it we can understand that the name should be unique and after a little tracing , it looks like some one changed the Next number in the WH/OUT Sequences to 1,after changing it back to it's proper value,the issue has been fixed.
in your case you should look for the sequence with the prefix WH/IN/
I hope this would help somebody.