There is a region in many AS phage (typically around 18 - 23 kb) where genemark and glimmer call different genes on different strands. These genes often have very large or complete overlap. This is unusual in the extreme and finding the proper strand is a known weakness of these ab initio gene finders. As such be very suspicious of genes which overlap and are on two different strands. To call both you need very strong evidence, ideally mass spec results showing translation of both frames. However extremely high quality HHPRED hits for both potential predicted protein products might also suffice. Without extremely strong support, review the evidence and pick one gene and delete the other following the rules as outlined in the annotation guides.
Edited yesterday, 21:53