If it’s happening only at turnouts watch when the train crosses the frog. Keep an eye where the tracks converge. A flange might be hitting. If this is happening a small file or dremel can be used to widen the gap just a bit to fix the problem. It’s pretty common, especially if the loco has a wheelset out of gauge.
If your turnouts have insulated frogs, check the other end of the frog (from the picture above), where the two stock rail come together to see if the wheel is touching the opposite rail. If this is the case, try painting some nail polish a 1/2’ or 10mm back from the frog and try running the train again. Some of the European wheels have rather wide treads. A permanent solution would be to cut a new insulating gap.
I may have missed it but I didn’t read what kind of turnouts you are using. I had a similar problem last year when testing out my first DCC layout. To make a long story short (no pun intended), I had 4 generations of Atlas turnouts in use. The older ones have little separation at the frog point where the two inside rails come close together. Some steam locos drive wheels were briefly touching both of them, and a short resulted. On DC, it was never a problem. Anyway, the only sure cure was to replace them, and all is well.
