@kani1 Can you check with one of the user for which you did not provide any access (entitlement) from SailPoint request center? what I am assuming is, may be it is happening because of sticky entitlement as I have mentioned in your other post.
If not, please check if the account is getting deleted in the target end before running the aggregation. What might happen is may be account is getting delete from ISC but not from target and in next aggregation it is bringing it back.