I've had a badly upset stomach after my last two runs (13km on Sunday; 8x800m intervals on Tuesday). I haven't experienced it before and I don't think I have changed anything in pre-run eating patterns. I may be eating too much bread. It's annoying.
Welcome to my world. I'm yet to identify what food is disagreeing with me (other than really obvious things like 2 litres of fizzy water, yes I'm an idiot) - the only way I can reliably avoid an upset stomach is to run without eating anything at all before hand.