When any entity (including a player) rides a vehicle, its hitbox has still the same size. This is mostly problematic for boats and minecarts as there you would be able to attack a player from underneath a boot or as seen here a player could get "for no reason" damage.
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Confirmed for 16w07b

Is this still an issue in the latest snapshot 16w44a? If so please update the affected versions.
This is an automated comment on any open or reopened issue with out-of-date affected versions.
Can confirm for MC 1.12.1.

Can confirm for 18w30b.

Affects 18w31a. Better steps to reproduce: Sit in a Minecart, press F3+B, then F5 and teleport the minecart up: "/tp @e[type=minecraft:minecart] ~ ~20 ~"
The Player Hitbox changes when flying or swimming, so this Issue should be attended too.

Confirmed for 1.13.1.

Confirmed for 19w37a.

Confirmed for 1.16 pre-release 3

In 1.16.4 and 20w46a
Can confirm in 21w03a.
Can confirm in 21w05a.
Can confirm in 21w05b.
Can confirm in 21w06a.
Can confirm in 21w07a. Video attached.
Can confirm in 21w11a.
Can confirm in 21w13a.
Can confirm in 21w15a.

Can confirm in 21w18a.

Affects 1.17
Can confirm in 1.17.1.
Can confirm in 1.18.
Can confirm in 1.18.1.
Can confirm in 1.18.2.
Can confirm in 1.19.
Can confirm in 1.19.2.

Can confirm in 22w42a

1.19.3.

Affects 1.20.1 Release Candidate 1