with a crushed coral substrate excess food etc. will fall in between the cracks where the cleanup crew can't reach it. this will decompose and cause higher nitrate levels compared to a sandy substrate. this sounds horrible, but don't blow it out of proportion.
you might have 10-15 ppm instead of 0-5. what you can do is make sure you have good flow across the bottom of the tank, a good skimmer, don't over feed, and when you do water changes-vaccum the top 1/4 to 1/2 inch of the crushed coral.
you can switch to sand if you want. it would be easier now than later. it's up to you.