Faradaic Efficiency refers to the yield of charges transferred toward an electrochemical reaction, in this case specifically the reduction and oxidation of water. Any other process involving charge flow without water splitting therefore lead to reduced FE. This could be side reaction(s) in solution (reducing or oxidizing something other than water) or reduction/oxidation of the electrode material or surface species. Measured electronic current through an external potentiostat cannot distinguish where the charges go, so only directly measuring O2/H2 can confirm FE. The best you can do without measuring the gases is to have a very good understanding of your electrochemical system to make reasonable assumptions about the presence of side reactions or corrosion processes.