If you have bobbin thread showing on the top the odds are that your tension is off, if it is only some times, your thread could be getting caught a bit on something pulling it tighter, it can do fine in most spots but direction and amount of fill can change that and pull the bobbin thread to the top, or the other cause may be that your bobbin tension is a bit loose,
Now if you do both sewing and embroidery with it, the weight of the bobbin thread could be different. usually you use a finer one with the embroidery and the tension may have to be adjusted going on to the other,
Now there is a fix as well for that as well, you can take a perminant marker (as close to the color you were using) and color the bobbin thread, when you do in the hoop projects you either have to change bobbin colors or color it in on the last part, it depends on the mood that I am in to what I do. I use prewound usually with the embroidery machine so prefer to use just white as they are harder to find in color and they are a lot more expensive.