There should be checks in place that immediately remove any sand on cells that cannot contain sand, seems that doesn't work properly. I'll look into it.

Hah, the checks were not firing if the affected cell is at 100% sandiness, that'll be why it doesn't work. I've pushed an update, report back if you experience any further issues!

Experiencing the same issue here, affected tiles are "deep water" and "shallow water", though those are the only two water types on my map, could be affecting more.

Okay, the original fix expected the mod "water freezes" to be present for sand to even possibly be on water. As there seem to be other ways of achieving this, I have removed the check for the mod and now cells are just always checked if they are water (and if so, the sand is immediately fully removed from that cell)