In the Harry Potter fandom, the explanation is always that A Wizard Did It. Usually, the distinct lack of mpreg in the books is for one of the following reasons:
To get pregnant, a man needs to drink a potion or use a spell. And who the hell would do that to themselves?
Male pregnancy is so incredibly rare that it almost never happens, which is why no one every mentions it. Usually, the two men have to be extremely powerful and/or soul mates.
There are a few examples of M Preg where the reasons behind the pregnancy actually makes sense in the context of story through a scientific or magical explanation. These, however, are few and far in between.
Sometimes can be justified when you're writing about a verse where there are characters that are not human. If the male getting pregnant happens to be an alien species or a youkai, then it could be explained that in their species, males are the ones to give birth.
Fanfiction has to make sense? What? I've stumbled onto fanfiction where it happens for no reason. Two guys have sex. Then a baby comes out. Because gay sex Totally Works That Way.
There's a crossover between the animated Teen Titans and the animated Justice League on fanfiction.net. As per the story, the Robin in the animated Teen Titans is Dick Grayson, and "Teen Titans" take place in the time between Batman The Animated Series and The New Batman Adventures. That's all well and nice...until Batgirl mentions Nightwing. WTF? If Dick Grayson is Robin, "Nightwing" shouldn't exist!
I don't think it's even stated when animated Teen Titans takes place, or for that matter if Robin is Dick Grayson (even the show's creators weren't even bothered who Robin was).
The Robin in Teen Titans is Dick Grayson (there are several things that indicate this, even though it's not outright stated, the least of which being Nos Yarkcid, Robin's counterpart from another universe). But Teen Titans is not part of the DCAU, which is where BTAS and TNBA take place. So, in the crossover mentioned, it makes perfect sense for there to be both Robin and Nightwing, as there would be two Dick Graysons.
That depends on whether it's really shown as a crossover between different worlds or if it just ignores that "Teen Titans is not part of the DCAU" part.
Peggy Sue and For Want of a Nail fics can be very well done. However, it just seems that too many times, there are a million coincidences that just seem to make everything work out well, which bothers me whenever I try to read one. In Peggy Sue stories, I understand that all of the foreknowledge that the character has helps, but what really bothers me is that, in fics without the foreknowledge, everything just seems to fall the right way. Why do all the problems seem to wrap themselves up nice and neatly and all this screwing with the timeline not cause other, unforeseen problems? This wouldn't bother me so much except for that fact that it shows up in even some of the best written fics of the genre.
When reviewers start their review with, "I don't normally like this pairing, but..." ...So, why did you read the fic in the first place? I said what pairing the fic was about in the summary, so why would you read it if you don't like the pairing?
The Theorem of Narrow Interests-Say you want to read about character x. You usually don't want to just read stories about character x but stories which are 1) readable 2) in a specific genre 3) interpret thecharacter in a certain way, 4) have specific kinks etc. There might not be many new good stories about character x that fit that criteria in your pairing of choice so you might take a look at other stories if they're well-written even if you don't like the pairing because beggars can't be choosers.