I cannot open overlapping entities. For example: AAI Depot (depot-chest)
It consists of three entities: Chest (invisible), Depot (a visual image on the surface), and constant combinator (invisible, at the corner).
Chest (invisible) and depot (an image), both have the same sizes and overlap each other.

Without this mod: If I click on the depot - it select and open depot chest's GUI.
With this mod: it trying to open depot's "image" GUI, but it does not have it, or non-interactable (nothing opened).

Looks like your mod change order of overlapping entities on the surface: which entity is above and which is behind the others.
Try to keep entities order the same.

AAI is unplayable now. The issue is the same for new placed depots too

Related: https://mods.factorio.com/mod/GhostOnWater/discussion/654a6e0ce7a3d658c7f48463

Report it to AAI. The fix for this is to change the entries selection priority and I don't want to override entity from other mods.
The reason my mod breaks things is becouse it changes collision masks for all entiies (to ensure the waterghost version still collides with regular entities) and the collsion mask is used as a tie breaker if the selection priotirty is set to the same value. The fix for this is to change the selection priority of overlapping enties like the AAI Depot, which is something that could be more easily done in AAI without it breaking anything.
Really mods should set a selection priority for overlapping entities instead of relying on the collison mask to select the right entity.
Also I'm no longer updating this mod becouse Factorio 2.0 Adds this as a feature with it's super force build.

thanks for info,
lets wait for Factorio 2 - it will force the AAI to fix this on their side :D