I don't understand why you are getting that error since you only have one ORDER BY and it's not in the subquery; you aren't using a view, and it doesn't appear to be part of a derived table.
However, give this a try:
select count(distinct exposureid)
from iinstrumentidmaster
where exposureid in (select TOP 100 PERCENT exposureid from iinstrumentidmaster group by exposureid having count(exposureid) >1)
order by exposureid
-SQLBill