http://jsfiddle.net/dcryan22/GUH4A/
d3.select('body')
.append('svg')
.attr('height', 100)
.attr('width', 100)
.append('rect')
.attr('fill', 'red')
.attr('height', 100)
.attr('width', 100);
d3.select('body')
.append('svg')
.attr('height', 100)
.attr('width', 100)
.append('rect')
.attr('fill', 'blue')
.attr('height', 100)
.attr('width', 100);
An SVG shouldn't be overlapping another SVG. The example above, shows 2 basic and separate SVGs in the same Body tag.
My guess is that you are somehow re-using the SVG canvas so that one renders on top of the other.