I applied the Rustoleum Epoxy Shield to my garage floor as a weekend
project. Followed all cleaning and temperature instructions to the
letter.

The floor has been curing for over 24 hours now, so I decided to walk
on it and bring some items back in. I used the colored flakes when
painting but sadly it seems like a ton of them didn't stick -- Is that
something that I did wrong? I lightly run a push broom over the floor
and end up with a HEAP of flakes. If I walk barefoot across the
garage, again, flakes all over my feet. Am I correct in assuming that
at this point, I may as well sweep the floor hard and get up any flakes
that haven't fully cured into the paint, or I'll just continue having a
mess later? I must admit I thought the flakes would get integrated
into the paint much better, and I didn't wait more then 3-5 mintues on
a wet spot before tossing the flakes on.

Thoughts?

Sounds like you went heavy on the flakes. Sweep up the extra. Flakes
can't stick to flakes so you must have the floor covered with flakes.
If you don't have many that did stick then the epoxy set up before you
flaked it.