Minecarts will appear on the wrong level when the rails go up 1 block and bellow them is another set of rails connecting to the ones at ground level. It glitches the minecart so it looks like it is on the bottom level when really it is on the top level. Using the hitbox viewing feature with F3 + B the hitbox stays on the right track yet the visual representation for the minecart does not.
I built 3 different examples but they all do the same thing. Detector rails do not detect the "ghost" minecarts as the hitbox doesn't actually pass over the detector rail.
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Affects version 19w46b

Affects 1.16.1

Affects 1.16.2 Pre-release 1
Also relates to MC-2783

Affects 1.17.1-pre2

Can confirm in 1.17.1.

Just reproduced it in 1.19.1 java edition single player
Duplicate MC-230738 has a nice video of how it looks.

can confirm in 1.20.4, attached video demonstrating the behavior

Affects 1.21 Also seems like it may be more than visual as hopper minecarts were able to put items into hoppers on the lower track
Fixed in the 24w33a+ minecart experiment. The minecart model now properly stays inside of the hitbox, so there is no visual issue anymore:
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