Well, I already noticed this in some levels, but only sporadically. The lemming position marker is certainly not completely absent from the experimental player, because I do get them in the first Nepsterlems level.
My current guess is: The bug is most likely not restricted to the experimental player, but I haven't yet found a reliable way to recreate it in the normal NeoLemmix player. My guess are problems with levels without hatches, while you haven't even played one level that has a hatch, or something like this.