Custom css is not applying to bootstrap subtheme
In the Theme settings Under Bootstrap Settings, Go to Advanced -> BootstrapCDN and choose Disabled from the dropdown.

Then in the theme info file uncomment the Method 1 section. Download the bootstrap files from Bootstrap Download and extract it to the subtheme folder. The extracted folder should be named - bootstrap and should contain all the necessary bootstrap js, css files.

You may get more info from this link Bootstrap sub-theming "how to"