Those dots of thread peeking through are what we in the longarm business call 'pokies'. Unless you're using a fairly thick batting, it's pretty much the nature of the beast. This is why I almost always match my bobbin thread to the top color. After all, if we were hand quilting, we'd be using the same color thread top & bottom
You could try using a thinner bobbin thread, sometimes that helps the stitches 'lock' in the batting better.
You could also choose a thread color that is mid way between the two colors - maybe a brownish? Then it will still be subtle on both the red and the black.
Andi