It's a bit hard to tell what could be happening. Can you provide a bit more detail about this and a short example?
Depending on how your app and html template is structured, my first guess (or element to check) is that there may be some missing css classes in your form which shiny uses to link the client and server. For example, shiny-bound-input or action-button. But it's a bit hard to tell. Are you injecting shiny elements into the template as described here or are you using your own html markup? You may also want to check your message handlers to make sure all the element IDs and message names match.
If you have some sample code that you can share, I'd be happy to take a further look.