It's hard to say with certainty, this would be easy to confirm by stepping through the code in a debugger.
But what looks suspicious to me is that you're iterating over arrays of enemies/bullets, and in the middle of doing that, you delete elements from the array and decrement the counter variables. Generally, when you need to iterate over something and potentially remove elements from the thing you're iterating over, you should do that iteration in a backwards fashion. That way changing the length and contents of the array in the middle of the loop is harmless.
for (var i:int = enemeies.length -1; i >= 0; i--)
{
// do your stuff and remove elements from the
// enemies array at will ... just splice the current
// element at index i out here, don't decrement i as
// you've done in your code above it will get decremented
// by the for loop
}