Removing Multiple Objects from Javascript Array Breaks Half Way Through

Because the length of collection will change, the trick is to loop from rear to front

for (var index = self.collection.length - 1; index >= 0; index--) {
    k = self.collection[index];
    if (fbContactIDs.indexOf(k.id) > -1) {
        self.collection.splice(index, 1);
    };
}

You should not change the length of an array while iterating over it.

What you're trying to do is filtering and there's a specific function for that. For example:

[1,2,3,4,5,6,7,8,9,10].filter(function(x){ return (x&1) == 0; })

will return only even numbers.

In your case the solution could then simply be:

self.collection = self.collection.filter(function(k){
    return fbContactIDs.indexOf(k.id) > -1;
});

or, if others are keeping a reference to self.collection and you need to mutate it inplace:

self.collection.splice(0, self.collection.length,
                       self.collection.filter(function(k){
    return fbContactIDs.indexOf(k.id) > -1;
}));

If for some reason you like to process elements one at a time instead of using filter and you need to do this inplace a simple approach is the read-write one:

var wp = 0; // Write ptr
for (var rp=0; rp<L.length; rp++) {
    if (... i want to keep L[x] ...) {
        L[wp++] = L[rp];
    }
}
L.splice(wp);

removing elements from an array one at a time is an O(n**2) operation (because for each element you remove also all the following ones must be slided down a place), the read-write approach is instead O(n).