The most common problem caused by the machine is incorrect thread tensioning. Improper tensioning can lead to bobbin thread showing on top, loops forming in the topstitching, and outlines that don't line up, especially running stitch outlines. It's imperative that you know how to set proper tensions and that you do so as needed.
Sewing tensions are affected by a number of variables, such as the color of the thread, how tightly wound it is on the spool, and how much is left on the spool. Also, if dirt and lint build up along the thread path, it can affect the tension as well. And though you may have an ideal tension setting, you sometimes need to adjust it based on the item being sewn. (One of our machines sewed much better on caps if we loosened the upper thread tension slightly. That's not to say this applies to your equipment, but we found it to be true with some of ours.) The thickness of the fabric will affect the sewing as well. While you should attempt to compensate for this in the digitizing process, adjusting your thread tensions may improve the quality of the sewing when dealing with thicker fabrics.
Another machine issue that can cause poor quality sewing is an improperly mounted hoop. Each brand of machine is a little bit different, but with most, it's possible to mount a hoop without getting it latched in place tightly. In some cases the hoop stays firmly in place, it's just not straight, which causes the design to be crooked. In other cases the hoop develops a bit of "play" or bounce, which will lead to all kinds of creative problems. Always double-check that the hoop is installed securely and properly. Give it a slight tug.
This is especially true with older caps frames. In fact, with cap frames, a design that is too tall can cause a major registration problem. You may find that it "fits" within acceptable cap design parameters and assume it's ok. But for low profile caps the crown is obviously not as tall as on golf caps. As the sewing approaches the top of the design, the cap is moved physically closer to the machine so that the end of the sewing arm starts to push against the inside top of the cap. (Since the end of the sewing arm is hidden by the cap, you may not be aware of this.) As it pushes against the inside top of the cap, it begins to stretch the cap causing distortion of the sewing surface. This is a limitation caused by the cap construction as well as the machine design. Some machines have slightly longer sewing arms than others. Slight is the key word, as the sewing arm contains the bobbin assembly which has to be directly below the sewing needle. However, some machines have a slightly reduced distance between the bobbin case and the end of the arm. The only cure is to reduce the height of the design or perhaps place it lower on the cap, if possible. And of course changing cap brands may improve this situation as well. With some models of machines, the pressure of the sewing arm against the inside top of the cap is enough to "pop" the entire sewing frame loose from the machine, a nightmare in itself.
Along these same lines, different machines have different methods of installing mounting brackets which mate to the frames and hoops. For example, if you are converting from flats to caps, you may to remove certain physical brackets and screws, then replace them with different brackets and screws. Occasionally, you may forget a screw, not tighten a screw, or overlook a firm seating for the brackets being installed. Once again, sewing quality will be affected. Along the same lines, you may have to change out needle plates depending upon what's being sewn. The wrong needle plate or a loose one can cause quality problems as well as thread and needle breaks.
Finally, there may be physical obstructions that limit hoop and frame movement. Maybe a loose object has fallen into the path of the hoop travel, blocking it or limiting it. (Ink pens are a major culprit.) On most machines, the sewing head attaches (vertically) to the sewing table. This of course is a built-in limitation for how far the hoop can travel vertically. However, most machines will allow sewing movement right up to the base of the sewing head. But if something falls into the space between the top edge of the hoop and the sewing head, it further limits or blocks the vertical movement. And, depending upon the machine, this may not cause a crunching, grinding noise, so you don't realize when it's happening. One common obstruction is the garment itself. Big, bulky items such as jackets and overalls may have sleeves that flop over into the path of hoop travel. Likewise, bulky items may catch on the needles, presser feet, or trimmer assemblies, any of which can limit proper hoop movement.