Dimensional accuracy

I am relatively new to 3-D printing and I am trying to hone the limited skills I have by creating nuts and bolts using Fusion 360 to model them. I’m printing them on an Ender-3 S1 Pro. But, I am having difficulties with the printed dimensions. I seem to have a consistent error of about .3 mm. The bolt head is .31 mm too big and the shaft is about .31 mm too small. I have the same problems with the nut to the point that they don’t match and cannot be threaded into each other.

Is this just something I need to learn to compensate for in my drawing or is there a problem with the printer set up?

If your using stock firmware look for step calibration, using a calibration cube etc. then check flow settings for the filament your using it will get those parts closer.

Also when designing threads make your nut a bit looser as you will always get ridges along the print that will throw them out a little and make them a bit snug

Completely normal. It’s like the reverse of “kerf” in woodworking. In 3d printing, if you draw a 10 mm diameter cylinder and then draw a 10 mm dia hole in a solid block, the slicer follows the center line of both the cylinder and the hole. It is up to you to compensate for the nozzle width. Actually, half the nozzle width. How you do it doesn’t matter. One way is to just draw both actual size, then scale the nut up in x and y (not z) to get the clearance. Another way is through xy hole compensation in the slicer. Or whatever.
Anyway though, the number you have arrived at yourself (0.3mm) is spot on. 0.25 mm is kind of a standard for fitment of different parts, a threaded bolt and nut would need a little more.
But anyway, you are good to go as is, you just have to compensate yourself.

Thanks guys, that does clear up things and I will give all that a try.