I tried this on an LG Fortune and an iPhone 5S. It only happened on the iPhone. Those are the only two phones I have and the virtual keyboard doesn't appear with the simulator. It does the same thing on Safari and Chrome.
With an iPhone 5, go to this site. Click OK on each of the two introductory dialogs and you'll be on a page with a react-select Search box and expanded list. Type "so" into the Search box. The list should scroll properly as you swipe up. Now type "sou" into the box. The list will not scroll. Instead the element underneath it will scroll. You can see this scrolling in the crack between the react-select's input box and list.
I think it happens when the list is a particular length - vertically shorter than the available space without the virtual keyboard (scrolling not necessary), but longer than the available space with the virtual keyboard (scrolling is necessary).
So it would seem that the phone checks the list length before displaying the virtual keyboard, decides that this list fits on screen so won't need to be scrolled. Then it displays the virtual keyboard, covering up part of the list and thus making scrolling necessary, but it doesn't send swipe events to the list to scroll it. Instead it sends them to the element underneath it.
Is my theory right? How can I fix it? Thanks