Forgive me if this has been said before or if there's already a work around. Basically, I use combination geological/gravitational survey ships with primary orders of 'Survey Next Five System Bodies' and secondary default orders of 'Survey Next Three System Locations'. This works fine for surveying system bodies, but once it runs out it triggers an 'orders not possible' message every time it finishes surveying three JP Survey locations.
My suggestion is just to make it so that if a ship cannot perform its primary default orders then have it perform its secondary default orders, and shunt the secondary orders into the primary slot so that it doesn't display a 'Cannot Perform Orders' message every few days. Of course this might conflict with some other forms of default orders I'm not thinking of, so perhaps add a check box for this option.