Самое простое решение - переместить GIF в SVG, чтобы вы могли надежно выровнять круги наложения с отверстиями пути клипа.
svg {
width: 100%;
}
.overlay path {
fill: red;
fill-opacity: 0;
}
.overlay path:hover {
fill-opacity: 0.5;
}
<svg viewBox="0 0 500 500">
<defs>
<clipPath id="myClip" clipPathUnits="objectBoundingBox" transform="scale(0.00991, 0.01)">
<path d="M 63.369194,12.267001 A 12.607063,12.267001 0 0 1 50.762131,24.534002 12.607063,12.267001 0 0 1 38.155067,12.267001 12.607063,12.267001 0 0 1 50.762131,0 12.607063,12.267001 0 0 1 63.369194,12.267001 Z" />
<path d="M 100.85033,12.267001 A 12.607063,12.267001 0 0 1 88.243263,24.534002 12.607063,12.267001 0 0 1 75.6362,12.267001 12.607063,12.267001 0 0 1 88.243263,0 12.607063,12.267001 0 0 1 100.85033,12.267001 Z" />
<path d="M 25.894252,12.267001 A 12.607063,12.267001 0 0 1 13.287189,24.534002 12.607063,12.267001 0 0 1 0.68012524,12.267001 12.607063,12.267001 0 0 1 13.287189,0 12.607063,12.267001 0 0 1 25.894252,12.267001 Z" />
<path d="M 63.369194,49.877972 A 12.607063,12.267001 0 0 1 50.762131,62.144973 12.607063,12.267001 0 0 1 38.155067,49.877972 12.607063,12.267001 0 0 1 50.762131,37.61097 12.607063,12.267001 0 0 1 63.369194,49.877972 Z" />
<path d="M 25.214127,49.877972 A 12.607063,12.267001 0 0 1 12.607063,62.144973 12.607063,12.267001 0 0 1 0,49.877972 12.607063,12.267001 0 0 1 12.607063,37.61097 12.607063,12.267001 0 0 1 25.214127,49.877972 Z" />
<path d="M 25.214127,87.216888 A 12.607063,12.267001 0 0 1 12.607063,99.48389 12.607063,12.267001 0 0 1 0,87.216888 12.607063,12.267001 0 0 1 12.607063,74.949887 12.607063,12.267001 0 0 1 25.214127,87.216888 Z" />
</clipPath>
</defs>
<image xlink:href="https://media.giphy.com/media/3ornk23QkOZcd32kjm/giphy.gif" width="500" height="500" clip-path="url(#myClip)"/>
<g class="overlay" transform="scale(4.955, 5)"><!-- 500 * the scale transform values in the clipPath -->
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 63.369194,12.267001 A 12.607063,12.267001 0 0 1 50.762131,24.534002 12.607063,12.267001 0 0 1 38.155067,12.267001 12.607063,12.267001 0 0 1 50.762131,0 12.607063,12.267001 0 0 1 63.369194,12.267001 Z" />
</a>
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 100.85033,12.267001 A 12.607063,12.267001 0 0 1 88.243263,24.534002 12.607063,12.267001 0 0 1 75.6362,12.267001 12.607063,12.267001 0 0 1 88.243263,0 12.607063,12.267001 0 0 1 100.85033,12.267001 Z" />
</a>
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 25.894252,12.267001 A 12.607063,12.267001 0 0 1 13.287189,24.534002 12.607063,12.267001 0 0 1 0.68012524,12.267001 12.607063,12.267001 0 0 1 13.287189,0 12.607063,12.267001 0 0 1 25.894252,12.267001 Z" />
</a>
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 63.369194,49.877972 A 12.607063,12.267001 0 0 1 50.762131,62.144973 12.607063,12.267001 0 0 1 38.155067,49.877972 12.607063,12.267001 0 0 1 50.762131,37.61097 12.607063,12.267001 0 0 1 63.369194,49.877972 Z" />
</a>
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 25.214127,49.877972 A 12.607063,12.267001 0 0 1 12.607063,62.144973 12.607063,12.267001 0 0 1 0,49.877972 12.607063,12.267001 0 0 1 12.607063,37.61097 12.607063,12.267001 0 0 1 25.214127,49.877972 Z" />
</a>
<a xlink:href="http://www.stackoverflow.com/">
<path d="M 25.214127,87.216888 A 12.607063,12.267001 0 0 1 12.607063,99.48389 12.607063,12.267001 0 0 1 0,87.216888 12.607063,12.267001 0 0 1 12.607063,74.949887 12.607063,12.267001 0 0 1 25.214127,87.216888 Z" />
</a>
</g>
</svg>