This one has been bothering me for quite some time.
Please report it here: Apple - Logic Pro - Feedback

Steps to recreate behaviour

1. Record some audio or drag a loop into the tracks area. 4 measures is enough.
   
2. Option-drag the track header down to the empty area to duplicate both the track and region (This step is just used as a confirmation.).
   
3. Zoom into bar 3 on the first region. Zoom all the way into sample level.
   
4. Move the playhead somewhere between 3 1 1 1 and 3 1 1 2 just to make the effect more obvious.
   
5. Split at playhead, use the marquee tool to cut, or the scissors. Any method will do.

Expected Results:

The region is cut and nothing more.

Actual Results:

The region is cut into two but the second region moves a sample or more.
The cut also creates a large gap between the regions.

To confirm

1. Insert a gain plug-in on the second track and flip the polarity.
   
2. Press play and you will hear and see that the two tracks go from complete null to phasing when hitting bar 3.