There are a few locations where I have targeted a rat and found nothing, only to move up or down and floor and find myself targeting a phantom Tok Rat.

Rat A:

Here is the rat before I killed it, /loc at 1119 768 892.There is nothing in my target circle. Note that hovering over the target circle on my map says the rat is Above.

Here I killed the rat with a non-target ability (Vile Spores proc from Legendary Bloom) The /loc is 1120 800 897, I never saw a body. (almost the same spot, only the elevation is noticeable different)

Here is the loot from the rat, located at the same place the target circle was, but I cannot loot it (since the rat's body was technically upstairs, as far as my spells were concerned.)
Rat B:

I was in the lobby, target told me the rat was with me, but map shows the rat far away form me (as the Rat Hunter addon shows, it's in the post-Munch Maze hall, a place I couldn't reach at the time, so no body/loot to investigate)
Rat C:

I am standing in the chest room for the Math puzzle, targeting a phantom rat. I am at /loc 1407 768 898. Map tells me the rat is actually at about 1019 858
Rat D:

Accidentally shot a rat with a non-target spell (Mystic Archer) in the Bogling Sudoku room at about 1317 768 699

(Forgot to /loc the sparkles, but here's the rough spot)
Found it's loot just around the corner at about 1279 768 672