Enter 2 two quavers in voice-1 then go back and enter two identical notes in voice-2 (using Ctrl+i, Ctrl+2 to switch to voice-2). Second 2 notes will have handles pointed to the opposite direction of the voice-1 notes. Now double click on the handles point downward and try to move it up, the bottom handle turns blue to indicate the selection and modification. Two side note handles switch side, which is wrong.

Tested on version r2795. Please see attached images 1(before changes), 2 (handles moved to wrong side)

Used the same file, saved as MusicXML and let it read by the older version r2012 and retested the above case and it worked fine there.