My suspicion here is it's because the queued to-build ships are in just that, a queue. You go negative because the
next ship to be built would send it negative, and so it holds until that one can be built.
Fixing this is a SMoP (Simple Matter of Programming, heh heh heh) but is going to be more resource intensive. Every cycle they check for build orders, they'll have to recourse down the queue to see if there's anything to be built that
could be built with remaining fleet points, and build that. Of course, you'll get the painful side effect that doing so will actually put your negative balance even lower, which means you may not can dig out, depending. And it'll have to be done seperately for each ship construction building queue.
The current behaviour might even be
preferable for pure simplicity of explanation. "If your fleet points go neg, you won't be able to build anywhere" is easy to document and say. Explaining seperate building bubble-queues for each construction yard is a bit more complicated.
In that light, I'm actually in favour of keeping current behaviour and simply documenting it more clearly, converting a bug to a feature with one sentence.
