The Solution to this problem, tends to differ slightly from case to case.
The general way to solve it is to
1.) right-click the bootstrap pill and select inspect or inspect element if firefox
2.) copy the css selector for the rule that changes the color
3.) modify it in your custom css file like so...
.TheCssSelectorYouJustCopied{
background-color: #ff0000!important;//or any other color
}