So, no.
I did try again several more times and noticed that even in version 388 the issue is stil there.
But it's random! same process causing different results.
Process:
1. open a new project
2. copy the background from another construct 3 project (copy-paste from one windows to the other)
3. copy-paste another 2 sprites.
4. run game.
I did that twice, one has boxes, the other doesn't. I screenshot the results so you could see.
TRY 1:
TRY 2: