UPDATE: Demo of problem here: http://jsfiddle.net/fdB5Q/embedded/result/
From about 767px to 998px, the form fields are wider than the containing well.
Smaller t
I just came across this issue and a on checking the bootstrap docs for form inputs it states 'Use relative sizing classes like .input-large or match your inputs to the grid column sizes using .span* classes.'
My bootstrap row was set to span9 for content and span3 for the sidebar. Setting solved the issue for me, the input boxes remain within the sidebar as the screen size reduced.