columnas adicionales mysql con el mismo nombre de dos tablas

Usar AS palabra clave:

SELECT
  t1.user_id as t1_user_id
  ,t2.user_id as t2_user_id
FROM table1 as t1
INNER JOIN table2 as t2
  ON t1.entry_id=t2.entry_id
WHERE t1.user_id='%s'