Technically, it's bydesign.

But really, it's just godawfuldesign.

The bright borders are part of the background:

The dark borders, on the other hand, are defined in the CSS:

.nav li {
    border-left: 1px solid rgba(160, 50, 10, 0.3);
    float: left;
    margin: 0;
    padding: 0;
}

These don't align properly (yay boxmodel, random changes and stuff like that) and as such, this bug occurs.