For some reason, the game allows ships and/or fleets from different civilizations to occupy a subspace gate.  Also, if you are not at war with all of the civs that have ships on the subspace gate, you will not be able to attack the ships on the subspace gate with which you are at war.  You can perform missile and beam attacks on an enemy ship if you move it to the top of the stack, but you will not be able to directly attack it with you ships.

Here is a link to a game save that will allow you to see the issues:

https://www.dropbox.com/scl/fi/mtxhcr4y3lv6bhata0746/Save-Issue-4-Under-2.4.578621.GC4Sav?rlkey=bh5bqop4xda2dcxykci03xfki&dl=0

To recreate the issues, perform the following steps:

1. Load the above save file
2. Move to the bottom subspace gate in my home sector (see the first screen snapshot below) where there is a grouping of ships
3. Zoom in to where you can clearly see the ships around the subspace gate
4. Click on the ship sitting on the subspace gate
5. Use the up and/or down arrows in the box in the lower left-hand corner of the screen (see the second screen snapshot below)
   1. You should see that there are 4 ships on the subspace gate, with 2 of them owned by the Iconians and 2 of them owned by the Corporate Sector.  I am at war with the Iconians, but I am not at war with the Corporate Sector.
6. Select one of my fleets surrounding the subspace gate and try to use it to attack the ships on the subspace gate.
   1. You should get the dialog shown in the third screen snapshot below telling you that you cannot attack without declaring war on the Corporate Sector.
   2. It does not matter which ship is on top of the stack, you will always get the same message.

My suggestion for fixing the issue of allowing ships from multiple civs to occupy a subspace gate is simple:

Don't allow ships to land on a cell if it is occupied by a ship from a different civ, regardless of whether the cell is a subspace gate or not. You already do this for cells that are not subspace gates, why not for subspace gate cells?

My suggestions for fixing the attack issue is:

Whenever you attack a stack of ships and/or fleets, regardless of whether the stack contains only ships from one civ or it contains ships from multiple civs, a window should popup showing each of the ships and/or fleets on the target cell.  You should then be required to select the ship or fleet that you want to attack.  The normal battle logic should then be executed.

Another option would be to always attack the top ship or fleet in the stack.  That way you would select your target ship or fleet by clicking on the stack until the ship you want to attack is on top.