Original topic post is from Positioning of notes and prefixes in polyphonic styles
You're not doing anything wrong. Logic doesn't detect collisions between notes on different channels, nor does it automatically space them apart. You're doing everything correctly. Use the layout tool to get the space you need.
If you find it difficult to select one of the notes, select it in the event list (or piano roll) and temporarily shift it up or down an octave. Use the layout tool to move the note in the direction you need and then put it back to its original pitch. (There are key commands for shifting notes up/down an octave which work in any editor window.)