A small idea from one who doesn't conduct, but records a lot. I've sat through plenty recordings checking the scores whilst recording.
Always make the note on that section/instrument that has the problem. Write only on the top of the page, if it's a problem for the whole orchestra.
Make your own system of terminology. A circle can mean dynamic problem, a box can mean rhythmic problem, triangle is something something.
Assuming your score is on off-white paper printed with black (possibly laser) use a green or red (if you're colorblind, they are still the same) marker or pencil, so it sticks in the eye on page turn. I use a pen cause once recorded I don't really need the score anymore, but if you need it for the next day, you might want to go home and erase the points.
One note about recording: it doesn't help to start recording when you notice something. Record the WHOLE rehearsal and listen to it when you get home. Looking at the score and seeing your points a couple of hours later, will give you a good idea of what you heard and what they actually played.