Kyle,
You answered your own question when you said that you put some brood above
the queen excluder to entice the bees to go through.

The bees above the excluder who were nurse bees felt that there no queen
present and raised an emergency who went on her "nuptial" flight from the
upper entrance and came back to "HER HOME" via the upper entrance and started
laying.  When transferring brood, you selected a frame with OPEN brood (eggs
and larvae).  If you
had selected a frame of ALL CAPPED brood, the bees could not have raised a
new queen.

By the way, it was never me that discouraged beginners from using queen
excluders.
QUITE THE OPPOSITE, as a matter of fact, I think beginners are far better off
using queen excluders.  In spite of those that refer queen excluders as
"honey excluders",
Not only do I disagree with their analysis, but I want to positively know
WHERE the
queen is in a colony and NOT GUESS or HOPE.

Thanks for trying to LEARN when you are a beginner.  Too many people DON'T,
and
suffer all the problems that beeHAVERS seem to have.  KEEP LEARNING!!!

I hope I have helped.

George Imirie
Certified EAS Master Beekeeper
beginning my 70th year of Maryland beekeeping
Author of George's PINK PAGES