The linear solver of the tools seems to have problems with float rounding errors. It will regularly generate nonsensical chains like in my screenshot, where random nodes are isolated (like unpackage nitric acid) or produce byproducts for no reason (like Empty Fluid Tanks) with a quantitiy of ~0.

Since this is only happening with tools after 1.0 and the solver has not changed [I guess], I had the suspicion that it is caused by the new converter recipes. They change the "directioness" of the solution graph because every raw resource can be created in another way now. This gives a decision point right from the start. I was able to verify that the behavior is indeed caused by the converter recipes. The 0 nodes vanish if all converter recipes are disabled manually.

So I propose to actually make this the default setting of tools (converter recipes disabled) because it will cause less confusion and clutter. I think resource conversion is very rarely what players will do, given it is a Tier 9 technology and uses valuable SAM. So resource conversion opt-in instead of opt-out should be the default.