1) Competitive algae. When using open tanks, naturally occurring algae competes for resources and space.
2) Getting the oil out of the algae. It has to be heated and dried to extract the oil.
Sapphire will be creating gasoline directly, so it should be possible to extract the gasoline through distillation with solar energy using a solar thermal water heater followed by counterflow heat exchanger.
The solar thermal water heater would heat fresh water entering the system, to kill off anything in it, giving the engineered algae a head start.
The counterflow heat exchanger would serve two purposes. First, it would cool the fresh water before it enters production. Second, it would heat the algae that is done, to distill the gasoline.
A counterflow heat exchanger is a pipe within a pipe. Hot liquid flows one direction through the inner pipe, and cooling liquid flows the other direction, through the outer pipe. When the flow rates are adjusted properly, the liquid that needs cooling exits the system at about the same temprature as the cooling liquid that is entering the system and the cooling fluid exits the system at about the temperature of the hot liquid that is entering the system
Using the finished algae as a cooling liquid, the hot algae exiting the counterflow heat exchanger should be hot enough to distill the gasoline directly out of it.