DD has a milk allergy. Some bottles she would do fine but others she would be very fussy. She got more fussy after the bottle though and during breaks to burp. She would arch her back and spit up and it would come out of her nose. Between feedings sometimes she would be fine but more often she would constantly strain (almost like trying to take a poop) for hours on end. After about a week of the new behavior, she started getting little strings of blood in her poop. You would really have to look for them.
This is exactly what my son does. I have tried to bring it up to the doctor but they just keep putting him on reflux meds. The part that is really bothering me is the straining portion for hours on end. I feel so bad for him! They keep brushing it off every time I say something, and, like you said, I have heard that the blood in the stools are sometimes impossible to see. Is there a way to test for this? It's so hard to know what is "normal" and what is not