1. Hydrogen has very low energy content by volume. That means that it has to be very highly compressed, to 5000 or 10,000 PSI, for use in a FCEV.
2. Compressing hydrogen to that degree requires special expensive high-pressure pumps, along with high-pressure pipes and storage tanks. Dispensing stations also have to have such pumps, pipes, and tanks, which is one of several reasons why building a hydrogen filling station is so extremely expensive; construction costs are about $1 million for each dozen FCEVs serviced per day! And of course maintenance costs for such fueling stations will also be orders of magnitude higher than costs for a regular gasoline filling station, on a per-car basis.
3. H2 (the hydrogen molecule, composed of two hydrogen atoms) is so very tiny that ordinary seals won't stop it from leaking pretty rapidly. Special expensive seals are needed for storage of compressed H2, and even then there is some slow leakage past seals. In fact, the H2 molecule is so tiny that it will (very slowly) leak right through the solid metal walls of a storage tank!
Note this also means the fuel will be constantly, albeit slowly, leaking out of any FCEV which it's stored in.
4. Because compressed H2 has to be compressed to such a high pressure, existing pipe distribution systems for natural gas and petroleum can't be used to move H2. Generally, hydrogen fuel has to be moved using special (and again, expensive) high-pressure tanker trucks, which of course drives up the expense and the energy cost of distributing the fuel.