for every process in Snap 5.0 you have to first resampled S2 Images to the same spatial resolution (eg 10m). It doesn’t matter what you do (subset, mosaicing biophisical parameters or something else). You should use options Raster-Geometric Operations-Resampling. It should help
Even if you have selected only the 10 m bands, the Sentinel-2 MSI dataset contain bands at 3 different resolutions, and many SNAP operators can not deal with that.
The resampling operator just makes the dataset uniform in terms of grid size, and it is an unavoidable processing step in many workflows.
Hope resampling the dataset can be the solution,
I’m using 5.0 version. I chose to process the images separately as tif files, resample them and then stack the tif files on snap. It Took 20 minutes, fortunately i dont have to process a lot of images. Do you think it will run faster with those methods?