The bug
When you dismount a rideable entity in a two block high space, you'll take half a heart damage. This is caused because you get teleported half a block too high when dismounting a rideable entity.
Linked issues
is duplicated by
Comments

@Kumasasa I see how this is the same problem and I think that they could be fixed the same way by making the player get out on the mine-track and not next to it.

Confirmed for
1.8.4 I would suggest changing the summary to something like "Getting out of Minecart places entity / player half block to high" because that is the reason why you get damage
1.8.5 Confirmed for all vehicles (also pigs and horses)

Confirmed for
16w05a
Please update the report with the information provided in the comment above this one
Confirmed for 1.13.1.
Currently you get teleported half a block too high when using an end gateway. See MC-184093 for this bug.
Can confirm. Issue since ever. Maybe caused by the logic that the player is placed besides the track, not on the track, see MC-1489