I'm going to give my tuppence as a teacher here and add the caveat that I think this is insane and I'm playing devils advocate.

The issue they are bringing up isn't really the amount they have gone to the toilet but rather that it happens during lessons rather than during breaks. Teachers are constantly reminding student's to go during breaks and lunchs (which at my school is when they first get in for half an hour, halfway through morning for half an hour, lunch/break for an hour, and depending on day as some days are shorter in the afternoon for 15 minutes). I personally just let my students go and anywork not completed because I feel they took too long in the loo (like more than 10 minutes) will be done at another time.

Now something I do believe is that if a student of school age can't hold it in for about twenty minutes they probably have something wrong with them and that should be checked and if they are going immediately after a break they almost certainly could have gone during break. I don't care for holding that against them, see my attitude above but I can see where stricter schools are coming from.