When you FMQ, you are moving the fabric around and this is changing the amount of tension on the two threads. Unless you have a machine that can achieve and keep a perfectly balanced tension (some can, but most cannot) and you are sufficiently proficient at FMQ that you maintain and sustain perfect movement, I think it is next to impossible to use two colors without getting some dots on one side or the other here and there.
What others have mentioned, though, is that (probably depending somewhat on the batting you use) the dots disappear with the first washing as everything in the quilt, including the threads, adjust to each other. What you may want to do is take one of your practice swatches with dots, bind it, and wash it to see if the dots disappear.