Bob gets a Face Full of Alien Wing-Wong, so he suffers from some of the typical pregnancy symptoms (weight gain, increased appetite), but not others (morning sickness, mood swings). Overall though, it's more like parasitism than an actual pregnancy.
Bob is undergoing "sympathetic pregnancy", due to Alice's pregnancy pheromones or other physiological cues. He shows symptoms of pregnancy, but is not actually pregnant.
Bob is an alien, a fully-functional hermaphrodite, or of some other male pregnancy -compatible type of being, and is naturally capable of getting pregnant and carrying babies.
Bob is transgender; while he identifies as a man, his body is still physically female.
Alice is impregnated by another woman.
Alice is part of a species or universe where the males get pregnant (like a seahorse for example) yet somehow she ends up getting pregnant.
Double Subverted: But goes to the doctor when he doesn't get better, only to find that he's not only pregnant, but 3 months along.
A male seahorse writes a fanfiction about a female seahorse that ends up pregnant.note Which you can find here
The minute Bob becomes pregnant, he turns into an Uke/Camp Gay that looks and acts like he was created by the mind of a really bad fanfic writer. After giving birth though, he returns back to his old self and goes on to ask what happened the last nine months.
Zig Zagged: Some men (often Uke archetypes) are capable of becoming pregnant, others are not.
Averted: Nothing related to male pregnancy is mentioned.
Bob is somehow capable of bearing children, and he and Andy know this. They are Genre Savvy enough to know that male pregnancy could be problematic (see "Deconstructed"), so they use condoms and spermicide for Bob's safety. If they decide later that they want a child, they will see about adopting one.
Or, unable to bear children, they enlist the help of the local Mad Scientist to genetically engineer a child from their genes, or get the assistance of a doctor and a willing female friend or paid surrogate.
Conversed: Alice "I don't get this whole MPREG genre, if they want a baby, why can't they adopt it or something?" Carl "Maybe the author likes the idea of malekind learning of the hardships of female reproduction."
Implied: A month after having a one-night stand with a mysterious man, Bob begins to suffer from mild nausea and occasional mood swings. Not long after, Bob is Put on a Bus. We don't see him again until a year later carrying a baby in his arms and a few extra pounds around his midsection.
Reconstructed: Bob's physiology (either naturally or because A Wizard Did It) averts these problems: apparently, Bob has a fully-functional uterus in there somewhere, and his pelvis will somehow accommodate the birth (or he'll just have a C-section.) And of course, Bob eventually accepts his role as a parent...after the initial shock wears off.
Bob's pregnancy is difficult, he and Andy face scorn from others, the pregnancy was completely unplanned (and possibly unwanted), and this all takes a toll on Andy and Bob's relationship not to mention other aspects of life such as social status and connections to friends and relatives.
The pregnancy was unwanted, but Bob, remembering he was born from an unwanted pregnancy as well, decides to go along with it despite the risks because he was given this much as well.
An ultrasound or blood test reveals something wrong with the baby.