I was recently confronted with a code puzzle in the app in the first scenario, with 5 possible glyphs to configure. I guessed once and had 1 elder sign indicating a correct position, and 4 clue icons indicating correct glyph by wrong position. The next guess I got 5 elder sign indicators, but the puzzle didn't end! All I got was a buzzer noise, like i had guessed wrong.
What do I need to do? Is this a bug?

Sounds like one to me. Report it in the bug report thread. https://community.fantasyflightgames.com/topic/227053-mansions-of-madness-bug-report/

AH! What a nightmare! But also, that's some amazing guesswork, haha.