That sounds like it's just an error somewhere, since it works with one. But it's hard to find an error with just a description.
Can you make a stripped down version of just those routines to upload? (you may find the problem when you are stripping it down. Which happens a lot.)
My off the cuff plan of how I'd do it would be to:
1. Have the player mark each of the enemy to target.
2. Then "for each" on the marks, so it will cycle through each.
3. spawn a missile and give it an instance variable to hold the UID of it's target.
4. as the missile flies have it turn 1 to 3 degrees toward the target until it hits something.
I did missiles like that in Orbital Bomb Bounder, and I believe I had a sine affecting the angle, so they wobbled a bit in flight.