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I can reproduce the issue, so you aren't imagining it.
After a bit of testing I noticed it only seems to affect objects with Bézier curves. I tried it on rectangles and the Intersection boolean operation works perfectly, so I suspect the inaccuracy is due to fact that Bézier curves are not capable of creating mathematically perfect circles, at least not ...
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The blue shape is subtracted from the brown one in three cases. In the left the result is a group of 2 separate paths.
In the middle the result is a single path.
In the right the result is a compound path. It's the way how Illustrator presents paths which have holes.
Not asked: A path can be drawn with self cutting edge. It also can seem to have a hole, but ...
2
If the Minus Front operation results in a single closed path, it just returns a single path.
If it results in several unconnected paths, it returns a group.
If it results in a shape with a hole in it, it return a compound path.
If you hold down Alt while clicking the Minus Front button, you get a compound shape where the bottom path is "positive" ...
1
As @joojaa mentions in the comment....
Remove the new stoke and choose Object > Path > Offset and enter a value half the size of the stroke you removed.
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