Table headers position:sticky and border issue

You can add

.table {
  border-collapse: separate;
}

But unfortunately it looks bad, a better solution will be adding a workaround using a pseudo-element.

th:after,
th:before {
  content: '';
  position: absolute;
  left: 0;
  width: 100%;
}

th:before {
  top: -1px;
  border-top: 1px solid red;
}

th:after {
  bottom: -1px;
  border-bottom: 2px solid red;
}

.table-sticky-container {
  height: 200px;
  overflow-y: scroll;
  border-top: 1px solid green;
  border-bottom: 1px solid green;
}

.table-sticky th {
  position: -webkit-sticky;
  position: sticky;
  top: 0;
  z-index: 2;
}

th:after,
th:before {
  content: '';
  position: absolute;
  left: 0;
  width: 100%;
}

th:before {
  top: -1px;
  border-top: 1px solid red;
}

th:after {
  bottom: -1px;
  border-bottom: 2px solid red;
}
<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.3/css/bootstrap.min.css'>

<div class="table-sticky-container">
    <table class="table table-sticky">
      <thead class="thead-light">
        <tr>
          <th scope="col">Name</th>
          <th scope="col">Title</th>
          <th scope="col">ID</th>
          <th scope="col">Username</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <td>Malcolm Reynolds</td>
          <td>Captain</td>
          <td>9035749867</td>
          <td>mreynolds</td>
        </tr>
        <tr>
          <td>Zoe Washburne</td>
          <td>First Officer</td>
          <td>8908980980</td>
          <td>zwashburne</td>
        </tr>
        <tr>
          <td>Kaylee Frye</td>
          <td>Engineer</td>
          <td>6678687678</td>
          <td>kfrye</td>
        </tr>
        <tr>
          <td>Malcolm Reynolds</td>
          <td>Captain</td>
          <td>9035749867</td>
          <td>mreynolds</td>
        </tr>
        <tr>
          <td>Zoe Washburne</td>
          <td>First Officer</td>
          <td>8908980980</td>
          <td>zwashburne</td>
        </tr>
        <tr>
          <td>Kaylee Frye</td>
          <td>Engineer</td>
          <td>6678687678</td>
          <td>kfrye</td>
        </tr>
      </tbody>
    </table>
  </div>

The second solution

.table {
  border-collapse: collapse;
}

.table-sticky thead th {
  position: -webkit-sticky;
  position: sticky;
  top: 0;
  z-index: 2;
  box-shadow: inset 0 1px 0 red, inset 0 -2px 0 red;
 }

You can add

.table {
  border-collapse: separate;
  border-spacing: 0;
}