In evaluate, it would be nice to be able to ignore errors (-g) when extracting matches (-x). The manual clearly states that other export options will be ignored when using -x, so this is not an error, but it would be nice if this were possible.
In my specific case, I have a large SD file with a few meaningless molecules (just the element 'X'). Both molconvert and cxcalc can skip over the garbage neatly. Evaluate will complain but the -g option will allow it to continue. Since I really want to extract hits, I had to pre-filter the large SD file to remove offending structures.