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In Illustrator I can't align an object with a stroke with an object without a stroke. It keeps popping over out of alignment. How can I stop it from popping over?

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Turn off align to pixel grid on the Transform Panel. – Scott Mar 19 '14 at 2:23

I don't know if you can modify your stroke placement in your project but I would try aligning the stroke inside its object. The screenshot was taken in InDesign but the option looks the same in Illustrator. Hope this helps!

Aligning stroke inside an object

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This is 100% correct for closed shapes, but if the shape is not closed (for example, a line) then that option is not available. On top of that, if the shape is not closed and one adds caps to the stroke, then the caps are always popping over any alignment. – cockypup Feb 26 '14 at 14:22
@cockypup: a workaround for that would be to align the line, then add/subtract 1/2 the stroke width in the x/y axis as required. Not optimal. – horatio Mar 19 '14 at 15:26

This is most likely because the non stroked item and the stroked item are slightly differently placed in the pixel grid.

One of them is probably going to half pixels. The other is not. When you try to make them align, one will always push out to a pixel position that suits itself, which will be different than the other, and they simply can never truly lineup.

Try reducing the size of the shape without a stroke by just one pixel in both axis. This might force it to align with the edge of pixels instead of their midpoint.

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