When a Player exits a Minecart or a Boat, they appear not next to where the minecart or boat is, but up to 5 blocks away, which regularly leads to placements outside tunnels in caverns etc. and not on the railstation or landingplatform...
This only seems to happen when there is a suitable space for spawning into, but spawning underwater seems suitable.
Duplicate of MC-36482. Note that this has been corrected for version 1.7.4. Make sure that both client and server are running this version.