Ah okay. I'm not 100% sure, but I think this is a display quirk. Basically the build time in the class design window is not exact because the actual build time depends on the shipyard, for example a 10,000-ton yard has a 50% faster build rate than a 5,000-ton yard, if I remember shipyard mechanics correctly. So if you built a 5,000-ton ship in a 10,000-ton yard it would build more quickly.
So the build time in the class design window should be giving you the build time out of a shipyard which is the same size as the ship, that's the only sensible way to calculate that value. Most likely what is happening is that adding engineering spaces increases the ship size more rapidly than the BP cost, since engineering spaces only cost 10 BP per 50 tons, IIRC, and you've got a ship that costs 45k BP per 60k tons.
As long as the actual BP cost is going up correctly, there is no bug, it's just a display quirk.