From my stint watching these in the county I'm observing (same machines), there are marks which don't read well - and there is no warning they are not being read since people are allowed to skip races. The only warning is if NONE of the marks on a page are read (which is how I discovered what reads and doesn't).
Small marks (centered or off center), check marks, and Xs do not read well. Several ballot sheets with only two races read as blank, when it was clear that the races were marked - but not marked properly. (The corresponding first pages - with about 20 races - went through without complaint as long as the machine could read a single mark - the machines are programmed to do that so a manual override is not required every time someone skips a race.)
People who are not used to scantron type sheets do not necessarily complete the bubbles properly - and an elderly population is more likely not to have encountered these kinds of sheets anywhere it counted. Erased marks (light but complete) seem to read as if they are still there. Dark but less complete marks (like those described above) do not seen to be reliably read reliably as present. And I expect there is some variation from scanner to scanner - so if the ballots were scanned on a more sensitive machine the first time, then rescanned on a less sensitive one for a recount, votes could "disappear."
If I ruled the world, I would require a visual once over of each ballot and set aside any ballots with less than complete marks for remaking with complete marks before being scanned