I think you might be running into a problem that I did when I first tried the construction rules. Namely that certain size ships hav a -1 modifer on certain systems. Take the Defiant-class (it was the one I first reversed engineered.) When you take into account that as a Heavy Escort it gets -1 for all its weapons...Which I think, if you will check, brings the Defiant to exactly 0 space left over. These rules are kind of hard to find, they are in fine print under the various system charts.