Could it be that your code is running in a way that it checks for button presses at a certain time in the main loop and it doesn't register if the button is pressed when the code is not checking for it? It's unlikely to be the problem based on you guys being unable to recreate the problem but something to check for.
Code:
// Sudo Code For Potential Problem
While (true)
Code
Code
Delay // Main reason button press gets missed
Check for button press Code
Code
Code
End While