Unexpected results exporting S2 bands as GeoTIFF files

The problem is that the BandSelect operator does not correctly consider the multi-size characteristics of Sentinel-2 data.
As you have found out, adding the Resampling operator fixes this. But for consistency you should not only add it before the 20m bands but also in front of the 10m bands. This should not slow down the processing drastically, because there is not to be resampled actually. In this example I mentioned it: