I am almost certain that Henk is right. I have seen this in my own sims. It's very easy for primitive evobots to shoot memory shots, in fact it is often an unavoidable side effect of first replicators since the most common method of reproduction I've seen in first replicators is just to walk through all the memory locations and increment them or similar.
I did do some investigation and found that surprisingly, shell and slime are not stored in sim files! (or teleported or saved with a robot in dbo files since then all use the same routine). This is why the yellow cirlces disappeared when you reloaded the sim. Fixed in 2.42.9t.