on some toy bids, when the bid is placed before it is confirmed, there is a popup which describes the possibility of toy recalls. This interferes with the snipe process on some snipe programs. I just sniped something that has the popup and am wondering if this will prevent the myibay program from sniping

That will not prevent myibay from bidding on those items.
If you sniped something already, you can check the status of your snipe to see the outcome.