Take a look at our Steel beam FAQ 
In it the first tip is to allow <25% composite action in the criteria so that you can evaluate beams as composite with fewer studs. Note, you have to assign the stud number and analyze as the program will never optimize a beam with less than 25% composite action when using US design codes.
If you want to allow any stud spacing, regardless of deck flute spacing, use a split or modified deck (Assign menu - Ignore rib spacing). Having a beam skewed to the deck such that only a few flutes cross any segment of the beam is likely the problem for some of those errors.
Finally, don't specify a max stud spacing that is too small to accommodate moderately skewed beams.