Many are certainly details... how the pipe penetrations are sealed, whether Styrofoam or dimple sheets are installed, what exactly the roof construction looks like (someone told us that in their case, covered plastic rather than wood was used for the roof), mineral wool or Styrofoam, thickness of the floor slab, windows max. 2 m wide, handling of special requests and planning changes or deviations, additional costs for electrical work, additional costs for plumbing, quality of gypsum plaster, underfloor heating or not, window profiles, roof tiles, solutions for structurally more demanding components (balconies, bay windows, overhangs), implementation of drywall construction, etc. etc.
Beyond that, certainly another 100 things that a layperson cannot even imagine...