There’s actually a combination of rules for design that can help you to set up your files so that the GFUI interprets them the way you want them to be interpreted.
First off, the computer can differentiate between different shades of green or blue much better than we can. We might think that we used the same shade of red on two different sections, but the program can see they are actually off by a couple of points. If they aren’t the exact same color, you’ll get a separate operation set up for it. (I do this one all the time.) 
That’s one thing.
Another is that fill colors are treated separately from stroke colors. If you have a filled vector shape in red, and a separate unfilled vector shape with the same red used as a stroke color, you will get a separate operation set up for it. The program is trying to interpret what you want it to do based on what you give it.
- Unfilled shapes with a Stroke color are interpreted as Cuts/Scores.
- Filled shapes with no Stroke color are interpreted as Engraves.
- Filled Shapes with a Stroke Color are interpreted as Cuts by default, since it’s not clear from the design what is intended.
So you get a separate operation set up for you depending on how you set up your file with fills and strokes. It’s not just about the colors used, although that is one of the main components.
Third thing - anything completely enclosed within a shape is treated as a group for moving purposes on the artboard. This is necessary because it’s easy to accidentally leave bits behind if they are not completely joined. (The CAD programs are notoriously bad for doing this.)
Fourth rule - each raster image embedded in the file is treated separately. That’s necessary because there are no other indicators to the program as to how each is to be treated.
These possibilities in combination make the program extremely powerful. You can do one engrave at one focal height, and another at a different focal height to achieve different effects. You can set up a filled vector, duplicate it in place and give the copy a stroke color with no fill, and set up an edge score for anything that you want to darken a little bit or to clean up the stair-stepping on a low LPI engrave. (I use the heck out of all of the options.) 
More detail on these in the Laser Design Basics tutorial.