What you have are the dreaded Pokies....It happens in free motion quilting as well. Take out your bobbin case and look at the little finger that stands up.....does it have a hole in it? If so, after threading the bobbin, put the thread through it and then insert and bring up to the top as usual. It has the effect of keeping the bobbin thread to the back of the piece rather than more balanced in-between. If you do not have that little hole then you must use a matching thread, try a bobbin thread like bottom line that is very fine and the pokies will be nearly invisible. Bobbin threads are more expensive than regular threads but worth their weight in gold. I use Bottom line in silver for just about all my quilting. It just disappears on the back, especially after washing. The added plus is that it is so fine a bobbin with it will last a very long time, much longer than a regular weight thread. It comes in all colors and small spools so it is well worth the investment in getting a selection, especially if you plan to do machine embroidery. Also it is great for hand appliqué, it just disappears into the work and is very strong so wear and tear will not harm it nor will it rot out as some all cotton can.
Just as a side note, you can make the pokies work for you, mix two, sewing weight, contrasting colors in bobbin and top thread say like a gold in the bobbin and red on the top. Machine embroider as usual and the mix will give you a bit of a gold speckle in the red, a pleasing effect...try it, you might find a new technique to add to your repertoire.