Non hai la funzione di aggregazione, quindi dovresti usare distinto e non raggruppare per
SELECT distinct SUBSTRING(`page_url`,-3) as pid
from `prop_log`
order by pid
e se ti servono solo le righe con cifra
SELECT distinct SUBSTRING(`page_url`,-3) as pid
from `prop_log`
WHERE `page_url` REGEXP '[0-9]'
order by pid
e per il numero di righe
SELECT SUBSTRING(`page_url`,-3) as pid
from `prop_log`
WHERE `page_url` REGEXP '[0-9]'
group by SUBSTRING(`page_url`,-3)
order by count(*)