trigger PopulateRegion on Shipment_Order__c (before insert, before update) {
for(Shipment_Order__c shipmentorder : Trigger.new) {
List<Ship_To__c> shipto= new List<Ship_To__c>();
shipto = [Select Id from Ship_To__c WHERE Ship_To__c.Ship_From_Zone__c = :shipmentorder.Ship_From_Zone1__c AND Ship_To__c.Name =:shipmentorder.Ship_From_Country__c ORDER BY Id LIMIT 1];
List<Ship_To__c> hubshipto = new List<Ship_To__c>();
hubshipto = [Select Id from Ship_To__c WHERE Ship_To__c.Ship_From_Zone__c = :shipmentorder.Hub_Ship_From_Zone__c AND Ship_To__c.Name =:shipmentorder.Hub_Country__c ORDER BY Id LIMIT 1];
If(shipmentorder.Hub_Shipment_Formula__c == False && shipmentorder.Ship_From_Country__c != null && shipto.size() > 0 ){
string region = Country_Region_List__c.getInstance(shipmentorder.Ship_From_Country__c).Region__c;
shipmentorder.Ship_From_Zone1__c = region;
shipmentorder.Ship_to__c = shipto[0].Id;
}
If(shipmentorder.Hub_Shipment_Formula__c == True && shipmentorder.Hub_Country__c != null && shipto.size() > 0) {
string region = Country_Region_List__c.getInstance(shipmentorder.Ship_From_Country__c).Region__c;
string hubregion = Country_Region_List__c.getInstance(shipmentorder.Hub_Country__c).Region__c;
shipmentorder.Ship_From_Zone1__c = region;
shipmentorder.Hub_Ship_From_Zone__c = hubregion;
shipmentorder.Ship_to__c = hubshipto[0].Id ;
shipmentorder.From_Hub_Destination__c = shipto[0].Id ;
}
}
}

Please change the line 29 to List<Ship_To__c> hubshipto = Database.query(queryString + whereConditionHub);