I agree with others that this looks like a tension issue, not knots.
If that photo is the back of the two fabrics, then those little "bumps" at each stitch are the links where the two threads, top and bobbin, link together. Those links should be inbetween the fabrics being joined, and not visible from either side. Since the "bumps" are on the backside of the joined fabrics, that is top thread which is being pulled down too far by the bobbin thread. If you can increase the tension of the top thread (do it in small increments, testing each time), then those bumps should disappear once the tensions between top and bobbin threads are equal.

Also try adjusting the feed dogs a littler softer. This looks more like a tug- pucker then a knot. Try re- threading the machine and using a needle for jeans. This may sound odd but they have a very sharp point and slide right throuh tight material. hope the info you get helps after you try everything. Let us all know what worked so we can add it to our own tip collection.
peace

If you are piecing I would use a 50 weight thread. I use Master Piece by Superior Threads. Aurofil also makes a nice 50 weight thread. The suggestion for a smaller needle to avoid leaving holes is a valid one. Try some samples after you have gone to a finer thread. If you are getting loops on the bottom you must either tighten your upper tension or loosen your bobbin tension. I would suggest tightening the top tension first. Even though your Saphire automatically adjusts for tension it is possible to override those settings. Check your manual or with your dealer on how to do this. Automatic cannot adjust for every circumstance. Be sure to write down how you changed it so you can put it back to normal when you are done with the batik.

some machines are just "picky" about what thread will work in them. I would keep a "journal" of what threads and needle sizes you used for projects and the results. Look for a pattern of what works.

When anything looks like that I always unthread my machine completely, including the bobbin. Check the bobbin area for lint and clean out that area. I reinsert the bobbin. Then I rethread the top thread of the machine. I find that it usually will correct the problem. But is I don't completely remove the thread it doesn't seem to work. Hope this helps.

Thanks so much for all of your wisdom ladies! I took out both the bobbin and top thread and vacuumed the bobbin casing. It helped, but I still had bumps. I think the thread is thicker than what I've been using. I pulled out my other thread and used that instead.

This time I had a very few bumps, maybe 5 on 45 piecings. I realize I shouldn't have any. I'm going to look into the tension settings and see if that solves it.

Thanks again ladies!

to Justabitcrazy...
The auto tension on a viking is just a suggestion/starting point. Go to the "set" menue and tighten the top tension by a few points. You may have to try a few different settings. When you turn off the machine and turn it on again it will reset itself to the auto setting. I know this because I own two Designer I machines and sold Vikings for two years.

Change your needle. You may have a very slight burr that is causing the bumps. Use the same size you have been using as a control to see if it makes a difference.