Reproduction:
Put a ship on a Hohmann transfer to the Mun. (Manually or with node executor, doesn't matter.)
Adjust your Mun periapsis to the altitude you want.
Open Maneuver Planner, select Circularize, select At Next Periapsis, and click Go.

Expected behavior: A node is created at the Mun PA which would circularize your orbit around the Mun.

Actual result: A node is created at the time you would reach your next Kerbin PA, as if the Mun wasn't there.

Workaround: Look at the time until Mun PA. Instead of choosing At Next Periapsis, choose "[ time ] from now". Enter the time to PA (say, "7h 20m 30s"), adjusting the value to give yourself enough time to finish typing. Wait until the time to periapsis matches what you typed, and click Go. The node created will properly circularize your orbit around the Mun.

It's possible that this may affect anything done "at next periapsis" when that will occur after an SOI change. Is there an easy way to test for upcoming encounters / escapes? Now that I think about it, this and "at next apoapsis" both might have similar problems if you're on an escape trajectory to a solar orbit, or from a moon to its planet. I'll try to test that soon.