Similar Situation for me this past weekend
flying with family and have four tickets for four passengers, including my 18 month year old. We boarded first, but near the end of boarding a passenger came on with a seat assignment for my 18month year old's seat.
Boarding passenger was stand-by (I asked her) and I told her the seat was already taken. FA came by and asked if that was a lap child, and I said no he isn't, GA came on too and I had to show my boarding passes. GA stated that the computer must not have scanned the one boarding pass and then left me and my family alone.
i had noticed the FA looking for empty seats earlier in boarding as well. On my return flight today, they then again asked if my son was a lap child or not during boarding. I also overhead the FA ask a young family the same question a few rows back too. It is almost like they don't even look at the manifest. My children even have MP FF accounts too.