Applying Lean system sounds to bring positive results all time. That won't be always the case. If lean is seen as a tool (not as a whole state of beeing and thinking) lean is like a sword, which can cause a lot of damage and suffering. Focusing only on reducing cost might lead to job cutting which will effect people involvement and increase resistance against Lean, whereas if lean is used to enhance product or service value, if it is focussed on the constraint and thus enhances throughput while raising productivity and reducing cost, it will cause a chain reaction of raising demand and competitiveness of a company. Therefore these things can not be considered as Lean fault as a system!! In my point of view I believe that they are kind of negative potential outcomes or obstacles rather than saying they are disadvantages. Lean system is some elements that can be filled from elsewhere such as Systems Thinking or the Theory of Constraints to support overcoming implementation obstacles. A good practice might be to let a group - employees for example- to figure out some future seen barriers and ask them in turn and list them on a flip chart being careful to identify each bitch/moan/obstacle with the name of the person that brought it up. Then asking them to come up with solution that each person answer his own problem. By doing that you will have both back up actions for particular problems with significant simplifications.
One critical issue was facing me in my past career was how to improve respond to customers needs and orders. Our focus was in enhancing technology we used and maybe modifying products we delivered. One great and interesting tool can be used in such situation is Lean. It focuses in reduction of waste and improving the Lead Time in order to achieve quicker respond, business setup and reduce delays as well. This is done that Lean investigates processes in deep to take out any non value added steps to have a smoother easy process with less cost and effective manner. By implementing Lean a company will become far more competitive in both the prices you can charge and the effectiveness of the services that you can offer thus enabling you to win more business and grow your business further.