There seems to be a bug in voronoi clipping; setting .clipExtent([[-1, -10], [width + 1, height + 1]])
works around the issue for these particular points.
xxxxxxxxxx
<meta charset="utf-8">
<style>
.voronoi-cell {
fill: red;
fill-opacity: .1;
stroke: red;
stroke-width: 1.5px;
}
.voronoi-mesh {
fill: none;
stroke: black;
stroke-dasharray: 1,2;
stroke-opacity: .5;
}
</style>
<body>
<script src="d3.min.js"></script>
<script src="https://d3js.org/topojson.v1.min.js"></script>
<script>
var width = 960,
height = 500;
var points = [[699.0050809085369,2.8436569264158607],[888.4805839508772,252.35402339603752],[610.3699017316103,447.0974076539278],[512.4963408708572,90.31530807260424],[563.3260828256607,250.2160455333069],[451.8548485636711,370.0483979191631],[619.8999966681004,237.06898477394134],[70.67834883928299,89.23503302503377],[138.53186666965485,443.46650049556047],[917.2623766958714,319.6419858140871],[835.7108900696039,178.92579676117748],[210.92742137610912,442.21618899609894],[239.4169557094574,171.82791873347014],[443.057961165905,201.0283146519214],[824.0466497093439,34.55296310130507],[723.5897192358971,40.55694455746561],[152.5887919217348,125.93188707251102],[298.39050337672234,356.05113685596734],[228.68067003786564,458.85977998841554],[354.60156485438347,372.44048540014774],[161.4455945044756,62.68311955500394],[829.1228798031807,371.91431783139706],[64.45855692029,16.175256459973752],[120.28321623802185,215.83681867923588],[923.2550290971994,275.6506217410788],[166.98800884187222,233.4072421072051],[102.34884694218636,136.21137070003897],[837.0920314639807,232.50216874293983],[116.36271581053734,413.76394394319504],[200.60938104987144,222.28361363522708],[567.5606162846088,77.06040609627962],[274.3246353417635,288.63093559630215],[254.2430106550455,213.86781835462898],[61.5095479041338,450.31107729300857],[36.59178413450718,237.1440433198586],[397.0605605095625,465.7969877589494],[834.3986919522285,172.6005991222337],[71.38201497495174,402.4498404469341],[672.1282913535833,249.62360912468284],[723.8617077469826,109.93840522132814],[751.8036069720984,68.9414587104693],[643.8624858856201,231.02924472186714],[242.00463496148586,149.44113383535296],[377.3637116700411,432.3011935921386],[793.6652635037899,458.6987466318533],[651.0418575257063,151.54773206450045],[448.5811297595501,253.67002771236002],[714.7731401771307,175.67026254255325],[121.73133283853531,62.08953191526234],[99.72131609916687,494.2970742704347],[449.95703659951687,453.9595516398549],[411.578684002161,183.46862692851573],[956.8594899773598,77.59027509018779],[612.1715218573809,46.03325598873198],[309.21511866152287,359.19026599731296],[804.4456478208303,45.493391109630466],[558.1986904889345,443.54945467785],[830.9829823672771,183.42329608276486],[427.7726800739765,158.21698831859976],[90.69512911140919,143.3550559449941],[813.8003895431757,69.5274363970384],[151.80836029350758,245.17876107711345],[314.3148458003998,430.0678597064689],[108.50703679025173,244.0565814031288],[46.95579819381237,383.270486141555],[8.339212462306023,432.2571096708998],[44.74743872880936,384.55081381835043],[548.7627111375332,256.79942849092185],[87.77389168739319,427.86694888491184],[716.1201567202806,50.134150544181466],[345.1531735807657,337.79136021621525],[717.5939214974642,466.216848581098],[285.67323312163353,301.9707479979843],[626.1467834562063,107.57232340984046],[306.58400796353817,282.19709394034],[216.67073495686054,120.48410973511636],[239.25122492015362,409.17698142584413],[644.6622573584318,354.13541609887034],[339.8401886969805,316.0193932708353],[251.0326612740755,190.29593898449093],[477.54173554480076,381.8539628991857],[261.6209629923105,364.0610105358064],[952.8780794888735,207.89624622557312],[910.0024218857288,105.64764111768454],[132.66220562160015,43.867148575372994],[956.9832441955805,293.3712595840916],[588.2194550335407,167.6968086976558],[690.3582617640495,252.01775517780334],[297.60200947523117,362.96630650758743],[818.3018396794796,430.22627115715295],[110.11742725968361,79.41011129878461],[29.421293288469315,461.2957357894629],[246.06291487812996,330.74483775999397],[349.722168892622,412.55073656793684],[905.9935462474823,103.25026756618172],[562.8941137343645,71.470781811513],[870.2599487453699,343.04971096571535],[276.9190192222595,38.70887157972902],[531.6803616285324,106.0691709863022],[349.0783931314945,215.77980741858482]];
var voronoi = d3.geom.voronoi()
.clipExtent([[-1, -1], [width + 1, height + 1]]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height)
.append("g")
.attr("transform", "translate(50,50)");
var topology = voronoi.topology(points);
svg.append("path")
.datum(topojson.mesh(topology, topology.objects.voronoi, function(a, b) { return a !== b; }))
.attr("class", "voronoi-mesh")
.attr("d", d3.geo.path().projection(null));
svg.append("path")
.datum(topojson.merge(topology, topology.objects.voronoi.geometries.filter(function(d, i) { return i & 1; })))
.attr("class", "voronoi-cell")
.attr("d", d3.geo.path().projection(null));
svg.append("g")
.attr("class", "voronoi-site")
.selectAll("circle")
.data(points)
.enter().append("circle")
.attr("r", 2.5)
.attr("transform", function(d) { return "translate(" + d + ")"; });
</script>
Modified http://d3js.org/topojson.v1.min.js to a secure url
https://d3js.org/topojson.v1.min.js