WMG / Genesis

The Lamb Lies Down on Broadway is about the wonders of childbirth.
Example One - All the illusions to "liquid". ("The liquid has congealed, which has seeped out through the crack"; "White liquid turns sour within"; etc.) Squick.

Example Two - Thinly veiled references otherwise pointing towards conception. ("He guesses he must be in some sort of cave... or eggshell waiting to drop from the bone of the womb.")

Example Three - Counting Out Time. Enough Said.

The Guaranteed Eternal Sanctuary Man from "Supper's Ready" and the televangelist from "Jesus He Knows Me" are one and the same.
He wanted to trick people into unknowingly supporting decadence, so he disguised himself as a televangelist, managing to get lots of people to fall for his trickery. It's only during the events of "Supper's Ready" that he's found out.

The titular home from "Home by the Sea" is Alcatraz.
There are many lyrics in the song that imply that people are being held in the home against their will (help us someone, let us out of here). Also, Alcatraz is on an island (a home by the sea).

The viewpoint character from "Misunderstanding" is also the viewpoint character from Led Zeppelin's "Fool in the Rain".
Since both songs are about someone waiting in the rain for their loved one and wondering where they are, it's not implausible that they're about the same person. If we put the two songs together, the story could happen this way: the man in the song waits in the rain for hours, and when his girlfriend doesn't come, he walks home. But as he's walking home, he realizes that he was waiting on the wrong block all that time, and so he tries to find his girlfriend...but by the time he does, she's found someone else, since she thought he deliberately stood her up, and the man she found was just finishing a date with her (or whatever "He was just leaving" was supposed to refer to) as the narrator found them.

So yeah, there very much was a misunderstanding...