I find that using different color threads top & bobbin is a real challenge to start with. As I get more confident (and competent) with free-motion I'm not so afraid to use a thread that shows versus tone on tone, and therefore am using the same color, or close to it on top & bobbin.
The other thing I notice at those turning points you describe, is if I linger at that point too long the stitches pile up and the bobbin thread is likely to show on the top. So, I'm learning to take my foot off the pedal at the turning point (needle is in down position), then start again in the new direction....a couple of stitches at slow speed, then speed up and keep going. Make sense?