You want sum rather than count - count will count records regardless of if they are 1 or 0.
proc sql;
create table mstats as
select actarm,country,
sum(case when ITTFL="Y" then 1 else 0 end) as rand,
sum(case when SAFFL="Y" then 1 else 0 end) as SAF,
sum(case when FASFL="Y" then 1 else 0 end) as FAS
from disp_ps
group by actarm,country;
quit;