Lower energy density than primary cells unless exotic chemistry is used. The energy density of a battery is limited by its open cycle potential, the concentration of active species and the number of electrons transferred during the discharge per mode of active species. As such, they can be triggered by known and unknown events to catch fire and explode. In addition to the above, danger of such events,  these fires are driven by the internal chemistry and are self sustaining thus they don't need oxygen to continue. 

Poorer charge retention. This is a result of the fundamental chemistry of the battery which gives rise to unavoidable chemical reactions which take place inside the battery during run time. These reactions impede the battery from maintaining full capacity throughout it's lifetime and their elimination is challenging and complex. A battery charge refers to the complete drainage and recharge of a battery. The more cycles a battery has completed the more it degrades, reducing it's lifespan. 

Safety issues. Secondary batteries especially lithium ion batteries are extremely sensitive to high temperatures and inherently flamable. These battery packs tend to degrade much faster than they normally would, due to heat. If a lithium ion battery pack fails, it will burst into flames and can cause widespread damage. Also many batteries such as button batteries, are small enough to be swallowed by children. This can cause serious internal injuries and even death. Small contamination such as ion metal impurities inside the cell, cannot be safely avoided during the manufacturing of batteries. Such impurities may cause short circuit defects and in the long run lead to thermal runaway during the over charging. 

Lack of standards. Standards ensure interoperability and compatibility between the many elements of a battery system. However, currently there is no one standardized format for a lithium ion battery. The battery cell format and shape is selected based on the users needs, which ultimately influences the design of the battery module. This is because of the view that standardization goes against the competitive nature of emerging technologies. 

High initial costs. This is because to pack more energy, cathodes need expensive materials like cobalt, lithium,  and manganese. So, the cost to produce an EV battery is high, which means they're sold for even more. Lithium ion battery packs comprise the metal lithium that has limited availability on earth. As a result, they are expensive but the process for extracting lithium and a relative lack of investment have yet to catch up with the rising demand.