This is happened because when first time the query is executed the native query is expanded from

update student set status=:status, modification_time = CURRENT_TIMESTAMP where id in (:ids)

To,

update student set status=:status, modification_time = CURRENT_TIMESTAMP where id in (:ids_0,:ids_1,:ids_2)

On executing next parameter set its still expecting the ids_2 even though there are only two values.