Can't start up a space station without all the trimmings! Just wouldn't be proper. Commander needs a comfortable chair and all that.
I think there are several issues here:
-Noting when a stalled construction order is being fulfilled.
I'm not sure how this helps.. there isn't much you can do if it isn't being fulfilled.
-Addressing negative resource amounts
This might be an actual bug.
-Multi-destination optimization of freighter routes/cargo
This is a tricky problem and may not be solvable given the calculation cost needed for an efficient solution, but perhaps it would be possible for a freighter, when it is deciding to bring a resource to a destination, check to see if there are other needed resources and if there are, and see if there are supplies along the way that could be grabbed with a quick detour. At the very least it should check to see if there is a pickup location that meets multiple needs and should prioritize scarce resource delivery over everything else. Calculating an efficient multi-destination route is of course a pretty intensive task, especially with multiple freighters doing somewhat redundant calculations. Nearest neighbor is probably the best option and the search would really only need to go one node out. Alternately, each resource hold could basically advertise what resources it has, and any construction process in need of resources would determine which sources are the closest. Freighters would then merely query the construction site and it would tell them what to pick up and where. Of course you already have some system in place, so it really depends on how well that could be integrated into a slightly more complex model.
My solution to the problem as explained is to optimize my freighters for different speeds/distances. I make the small freighter very fast with a long range and a smaller hold. This ship is meant to have a quick turnaround time so it is always quickly fulfilling smaller needs and moving on to the next, and it is also able to reach out to more distant outposts and other empires. The medium freighter is the general purpose freighter, nothing special here, but it tends to be the slowest sub-warp freighter and should have the range to reach nearby empires. The large freighter has a very limited range and huge capacity, while also being quick. By limiting it's range, it won't go off into the wilderness to supply some random outpost with 10 silicon, and will instead stay close to my core worlds transporting large amounts of core resources.