They aren’t appearing randomly. They are appearing when you have endpoints that are too close together.
It is very small indeed. If I were modeling this sort of thing I would first, use components instead of groups. Then I would either use The Dave Method or probably in this case I would probably just model it as if inches were meters.
What is the plan for the model once it is finished?
BTW, it seems kind of strange to me that you would model something this tiny using Architectural units and Display Precision of 1/16 in. I would just decimal units with higher precision and definitely turn off Length Snapping.
