Okay, found this. When I added the new shot impact dots in 2.42.7, I missed the case where the creation of a virus shot fails because the gene being referenced is beyond the end of the DNA. In Testlund's sim, bot 37 (and presumably other bots which display similar persistant dots) is attempting, over and over, to create a virus shot using gene number 10661, which is of course, beyond it's 11 genes. The creation of the shot fails as expected, but in the process of almost creating and then failing the creation of the virus shot, an erronous virus shot impact dot is displayed at the point of shot origin, over and over each cycle, as the bot trys to create a new virus each cycle.
Any bot trying and failing to create a virus will exhibit a dot for that cycle.
Totally harmless. Fixed in 2.42.8.
Also some of the bots eye dots are located inside the bots instead of sitting at the edge of the cell wall, where they should normally be.
This is an artifact of your monitor/ graphics adapter resolution/dimensions. The edge of the bots are displayed as perfect ciricles on the screen (because the underlying VB circle command is aware of your monitor resolution and adjusts accordingly and it is used to display the bot edge) but unless you are using monitor resolution dimensions with an aspect ratio of exactly 4:3 (e.g. 800X600) the bot's eye will be displayed on the true, actual, underlying edge which will not coincide with the displayed edge (the eye will trace an ellipse). If you watch the eye, it will touch the bot edge either at the top and bottom or on the sides, depending on whether you are using short and fat or tall and skinny monitor dimensions respectivly, then go inside the bot the rest of the time, tracing an elipse. Shot impacts will exhibit the same issue. Some shots will appear to go inside the edge and yet not impact. In reality, this is just an artifact of the way the edge is displayed on monitors with aspect ratios that do not exactly match the field dimensions - the shot did not actually go inside the bot, it just looks that way. The ellipse that the eye traces is the true bot edge and shot impacts only occur if they go inside that.
Don't worry, the underlying physics of everything is fine. It's just an artifact of the way bot edges are displayed using the VB6 circle command.
Some day I may implement custom field dimensions and this will get fixed as a side effect of that, but not today.