there is a demo, browse with ios6 device.
1 - when dom ready, touch the input element in iframe, focus on it.
2 - long touch until the magnifying glass show, release.
2 - input any word, the problem reproduce.
if remove touch module code from zepto, it works fine.
I suggest forking the touch module and adapting it to your needs (possibly preventing events from being handled when the main document doesn't have focus). I don't see how Zepto causes this specific problem as the touch module doesn't prevent any default events or propagation of events (possibly this is a browser bug or a security "feature"). Verified on iOS 7.0.3.
Because of being such an edge case, I'm closing this ticket. If a simple solution surfaces, we'll gladly add it to Zepto.