The yellow balloon which Debbie is trapped in changes size throughout shots. Particularly when the Klowns are entering the fun house at the amusement park, you can see that the balloon is significantly smaller than in the other shots.
After the Terenzi Brothers fall through the trap door and the others turn around to see them gone, Grant Cramer stumbles and almost trips over them. This is because the actors playing the Terenzi brothers only fell on the floor, not through it.
The goof item below may give away important plot points.
When the Klown blows his "blowout" at Moonie it is clearly above the horizontal bar of the cell door, the next scene where the "blowout" garbs Moonie by the neck and pulls him toward the cell, the "blowout is now below the horizontal bar.