Well after searching for days about this, I posted here and found my answer shortly thereafter.
This is a known issue in the internal Android Browser in Jellybean.
There is a workaround with some trade-offs. Such as losing the ability to scroll in text areas, but if you have this issue, then this is a good workaround.
The workaround is to add this to your main CSS file:
/*
Prevents a bug in Android 4.0-4.1 that duplicates text inputs onFocus ANDROID BUG# 30964
Link to Bug Tracker: http://j.mp/YhydH6
Remove when no longer needed...
*/
input {
-webkit-user-modify: read-write-plaintext-only;
}