I had the same issue and worked it out by nesting a div inside bootstrap col and adding padding to it. Something like:
<div class="container">
<div class="row">
<div class="col-md-4">
<div class="custom-box">Your content with padding</div>
</div>
<div class="col-md-4">
<div class="custom-box">Your content with padding</div>
</div>
<div class="col-md-4">
<div class="custom-box">Your content with padding</div>
</div>
</div>
</div>