Mario and Luigi BIS is this AP?

Sorry if this has been answered (I've trawled through loads of posts) but can somebody help?
My son has been playing through the patched version of M&L BIS and has defeated the boss who throws trash in Peaches Castle, when he goes down the pink pipe Bowser reappears in the top screen as if something is going to happen but nothing does is this part of the AP set up or is he missing something?

You should ask on the technical help thread here https://www.romulation.org/forum/index.php?topic=22731.1825. You might want to include more information such as which flashcard and firmware or emulator (no$gba, desmume, ideas etc) you are using. Some cards that support the clean rom have problems with the patched one so it may be just that.