The main issue is the risk your details can be wiped from the company's database. If there is a major system failure, information can be lost. This can include entire periods where bookings were made. This can cause problems when it is time to travel. The company may not have any record of your booking and can prevent you from traveling.
Electronic passes can be a hindrance if you are changing plans at the last minute. A common scenario where this can happen is when your original trip is delayed, and you cannot afford the delay due to transfers. Companies will then try to find alternatives for you. However, each company has their own rules regarding electronic passes. This can cause issues when you are trying to change from one company to another. 
Not all places will allow you to enter without seeing a return pass. Some countries will prevent entrance because of fears that you intend on staying illegally. Not all travelers with e-tickets will arrange to have a return pass. Some may want flexibility; others may want to wait for cheaper tickets to appear closer to their intended departure date. The flexibility of electronic passes can therefore be a disadvantage if you are traveling to some destinations.