If you would like to use non-modified MCE's in crates make sure you include one without the crate somewhere within the level.

For example you said you want smoke rings to come out of the crate when you shoot it but instead of that manny jazzes on airboard pop out and fly away.

Solution:
Include one such event with a generator (in this case "Trigger Rock") somewhere within your level. Usually somewhere at the top so the rising smoke ring won't bother you.