I don't know how this happens, but after playing with the bootply for some time. I have a fix.
I think what causes it is the box-sizing:border-box
at bootstrap.min.css (line 7)
.
Either changing that, or overriding it to box-sizing:content-box
seem to fix this issue.
If you have a custom CSS file, use the following class to override Bootstrap.
* {
box-sizing:content-box;
}