Sure, every PCR test of this kind as several problems, the most common problems being:

1. technical problems, as the primer recognition sites are variable;

2. the two genes expected to be arranged together are not.

I suppose you look for E. coli O157? Of course it is possible because you look for two independent genes. rfb is for the O-antigen gene and eae for intimin. So you cab have a strain rfb positive and eae-begative and vice versa. This has a priori nothing to do with the PCR you use.

best regards

Please look Prof. Lothar Beutin's answer that is completely right and very clear cut