Going to revive this old thread to say this is a constant issue for me in 2.3.0. It makes the tool almost unusable because I have to save and restart every few minutes. I am on Windows if that helps.

 EDIT: Immediately after sending this, I noticed I think it has something to do with scaled objects. I have a large scaled (50x50) cube beneath the play area so I can easily keep track of the bounds I can work within. That object is locked, but it appears to have click priority, so that object is receiving the click event and not the closer object. I attached a screenshot of the issue. If I click in the green area, it will click the correct object. If I click any of the objects in the red area, it will click the black square underneath instead of the purple cube.

EDIT 2: Also, the "Select through grid" setting does not appear to work.