When I was doing ear training, I found it's very difficult for me to distinguish some P4 and P5 intervals (harmonically), mostly around C3 or lower. For instance, if a perfect fifth, C3 and G3 are played simultaneously, it sounds more like C4 and G3 to me, which I think would be a perfect fourth. It seems difficult for me to hear the fundamental tone of C3, however I'm more sensitive to its overtones.
For higher notes this won't be a problem. Nor if it's a melodic interval (i.e. notes are played one by one).
What might have gone wrong with me? I use the "Complete Ear Trainer" app by the way.