Sorry, I'm not familiar with Crossfire, but I'm told it's pretty feature rich, so perhaps that is built in. In Crossword Compiler, the system immediately figures out which individual space has the fewest possibilities and starts there. But it may be a combination of entries in a particular sector that cause the problem. You can eyeball this by considering the number of entries that have multiple letters already forced by theme entries or others - this increases the odds of problems. Another factor is the nature of the letters - that is if there are a lot of high score scrabble letters in a section, it's likely to be tough to fill.
Another consideration is the word list itself, because if it isn't robust enough, many more sections will be tough to fill. There are good word lists on this site for members, and perhaps an even better one on xwordinfo.com for a fee.
And, finally, if you have a sector that you just can't seem to conquer, it may be time to add a "cheater" blank square, re-arrange the theme entries (if possible), or even redesign the grid. We all have to do some of all of those things once in a while.