This is very vague as I haven't investigated it much yet. The only things I can say are:
a) Most levels are not affected.
b) One way to consistently reproduce it is to play "Odyssey" from Lemmings Plus Omega II. In this, the Walker is drawn as an athlete-zombie on the skill panel. All other skills get drawn normally.
In NeoLemmix Introduction Pack, Rank 2 Level 14, the cloner displays one normal lemming and one zombie.
I noticed that too. The Cloner graphic partially uses the already-generated walker graphic while generating itself, so this is likely why.
Should be fixed in commit 7C2A824. This commit removes the only possible cause I can think of, and I can confirm the issue no longer happens on either of the two levels identified so far, though I haven't done extensive testing. I'll reopen this if it resurfaces during later testing.