i think this is not meant to be happen:
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draw a circle
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move the left handle from the top-point a bit to the left (or right)
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select this one and the left handle from the bottom-point
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hit cmd-A (to align these both handles)
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now the handles of the left-curvepoint also move, slanting the axis of the handles
(writing »left« was just an example, this happens on either sides)
reproduceable on Glyphs Version 1.3.25 (526) (OS 10.6.8 & 10.9)