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There are two puzzle rooms in the Black Tower.  The southern room is the one with the glitch.  I don't think it affected the story or gameplay in any way.  Maybe there was a nice prize if solved, but it certainly wasn't anything vital as is the case with the north room.  Before I found the miniguide, there were areas I crudely mapped out by hand (land, air, sea) and was thrilled to see those maps in the mini-guide.  The only other place I felt the need to fully map was the forest temple in the Depths.  All that teleporting around.  :)  That would be a nice addition.  

It's the chemist recipe I seem to have missed.   I'll be sure to find it on my next go-around.

Yep, you're right. I checked both puzzle rooms and realized one wasn't set up quite right, so this'll be fixed soon. The reward is a relic that grants lots of powerful skills, but certainly isn't needed to complete the game.

I'll make sure to upload a map of the forest temple when the game is released on Aldorlea. Thanks again for the feedback LadyJJ, and have a great day!