When exporting small circles to SVG (radius smaller than approximately 4?) Ipe only uses two cubic Bézier splines rather than four like it does for big circles. While the approximation with four splines is indistinguishable from an actual circle, the approximation with two splines makes for a "fatter" shape than a circle. The difference is small but visually noticeable: I found out about this behavior when I exported a logo with some small circles to SVG and noticed that the circles looked "off" in the SVG version.

To demonstrate, I created an Ipe file with two circles, one with radius 6.4 and one with radius 3.2. For both circles I added small marks positioned exactly on the circle. In Ipe these marks are indeed shown correctly:

After exporting to SVG and opening the result in Inkscape, it looks like this:

On the small circle, the marks' position deviates noticeably from the "circle":