You can't stop the problem because
I too, believe it or not, have the same issue lol

.
I actually think it's a sign that you are getting way too into it and pondering other possibilities instead of just going with the flow and enjoying it. I do that a lot with quite a few animes (but I suppose that's because I have an inquisitive mind).
Some animes i don't do it because it's interesting enough so much so that you look forward to what happens next and don't really have time to think about it mid-show. Perfect example is Code Geass. I don't think I did that with school days though. But I did actually hesitated to watch the NEXT episode after some .....bad/disturbing event had taken place like makoto's threesome was very upsetting and rather immoral from Sekai's perspective so I didn't feel very good about it. I kind of felt like "Oh I feel like shit now, feeling sorry for Sekai/Katsura. I know if i watch the next episode, it'll be bad and I know I'll make myself feel worse" kind of situation lol.
I stopped a few times in KGNE since some parts were so slow going. Other times it'll probably be from some stupid situation or some fanservice. I don't know why it makes me feel uneasy, it shouldn't lol.
Another time I watched Soul Link (which is a crapped up rip from the H-game) I paused a billion times. Dragonaut I paused a billion times so much so that I only finished watching it 2 weeks ago since following it from the very start. Maybe they were boring or unstimulating.
Never really thought about why I did this so deeply before lol.
Probably around start of College did I start watching anime properly because right now, the only spare time i get is on holidays

(so better make use of the time)