I have not done any puzzles with a rebus but I just tested out this feature on my copy of Crossfire and it worked okay for me. I'll list what I did in my simple test. Here's hoping it will help you figure out your problem!
I started with a blank grid and then I clicked on the Rebus tab. There's an "Add" button at the lower left of this tab. Click on this button and it will ask you to define a new rebus. I defined an easy rebus of 4 letters, STAR, with the user symbol S. This rebus was added to the list (you can define several of them) with a green "+" sign to enter it into the puzzle and a red "x" to delete it from the list.
Next, I selected an empty square in the grid and used the "+" button to add it to the puzzle. Finally, I checked the fill feature. Sure enough, it found words containing STAR even though all 4 letters were in only one square.
In case my description didn't help, here's the link to their web page for this feature - http://beekeeperlabs.com/crossfire/docs/index.html#REBUS