The bug
Lingering potions thrown on the ground can produce area effect clouds at varying heights. This behavior occurs from all kinds of throwing angles, distances, and speeds. This bug could be sufficiently fixed by fixing MC-88368.
Short entities like axolotls and turtles can sometimes avoid lingering clouds just because the cloud spawns so high, even though the potion landed on the ground. Example: MC-210987
How to reproduce
Press F3+B and throw several lingering potions on the ground. You can clearly see that some hitboxes are higher than others, often floating nearly half a block off the ground.
Related issues
is duplicated by
Attachments
Comments

Here you can see the bottom of the area effect cloud hitbox in comparison to a block. It is floating about 1/3 of a block off the ground. The potion was thrown directly downward onto solid ground. Other potions thrown in that way were placed at different heights.

I am able to reproduce, it probably depends on the angle you throw at. This bug has probably existed since 1.9, when lingering potions and area effect clouds were added.

The issue is linked to how the game extrapolates the path of a moving object. If the next update to the position of the potion makes it collide with a block at any time along its path, then the potion will break and spawn in the area effect cloud. The problem is that it uses the current position of the potion, not the extrapolated collision point, as the position to spawn the area effect cloud. Simply changing which position gets used should fix the issue, assuming that my theory is correct.

Confirmed as of 1.16.3.
Can confirm in 21w03a.
Can confirm in 21w05a.
Can confirm in 21w06a.
Can confirm in 21w07a. As stated in this report, this doesn't always happen so you may need to throw several potions down in order to reproduce this issue.
Can confirm in 1.16.5 and 21w08b.
Video attached.
Can confirm in 21w11a.
Can confirm in 21w17a.
Can confirm in 1.17.1.
Can confirm in 1.18.2.
Can confirm in 1.19 and 22w24a.
Can confirm in 1.19.2.

Can't reproduce on 1.21.4. This was fixed in 24w36a when MC-207101 was fixed. Currently clouds spawn at the height of any block or entity they collide with.

I have attached the behavior in 1.21.4.Youtube