Don't play bowling with the third boss! It causes a freeze!
Played on PAL 3DS, with the cartridge version of the game, if either of these facts make any difference to anything.
Randomly found during my first playthrough. If you use the bowling ball on the blooper boss, Gooper Blooper, the game will softlock. It doesn't seem to matter what circumstances lead up to it. A little silly because the bowling ball was a key feature of the third world, but whatever.
Nevertheless, it's a fun little game. Here's hoping this gets patched, since we know 3DS games can nowadays! Until then, just be careful not to bowl over the third boss. (I also read that the final boss doesn't work properly with bowling ball either).