You are removing item at the same time when you are enumerating same array. Use filter instead:
var array: [Int] = [0,1,2,3,4,5]
array = array.filter{$0 != 2}
or, for multiple values, use Set:
let unwantedValues: Set = [2, 4, 5]
array = array.filter{!unwantedValues.contains($0)}
Same in one line:
array = array.filter{!Set([2, 4, 5]).contains($0)}