Electrolytes/energy bars and stomach problems

Hi guys, just creating a new thread for this. I'm pretty new to cycling and at a low enough level. I generally drink some sort of isotonic drinks on the bike on longer rides, and maybe an energy gel, especially if there is climbing involved. I might also have energy bars/flapjacks the odd time and eat regular food. I'm usually pretty scared of running out of fuel and maybe I overdo it and get the balance wrong. It seems that the few times I've done longer cycles where maybe there's overnight involved so a few days cycling, it takes a while for my stomach/bowels to get right again. From stomach pains to irregular bathroom visits. I can only guess that it's taking large amounts of electrolytes and sugar, etc., wich I wouldn't quite be used to that is messing with my digestive system, maybe someone can shed some ligt on this also. My question is, is this very common, and how to other people manage, and any advice?
Thanks in advance guys