Bug 1:

Another pretty broken aspect...

In one play through, design a ship that uses a certain amount of capacity.

In second play through, when the technology to build the ship has been reached, you can now build that custom designed ship, irregardless of whether you have the necessary capacity tech to build it.

E.g. Can build ships with capacities that look like 280/250.

Bug 2:

With enough constructors, build everything there is to build in a starbase.

Note the remaining constructor points is now at 0.

When a new module becomes available, the starbase magically gets just enough points to build it.

...Now I can't tell if this is leftover points or if the base is magically creating new ones...Either way it is a bug, with the latter being more serious.