My first thought is why use an exclusion rectangle in ADE rather than just deleting the objects? You mention drawing a polygon - it is always a rectangle so I assume you are using the correct tool?
The preferred method in ADE is to delete objects in the display. This is particularly true if you are working from a stock airport. To understand how this works you need to know that when you load a stock airport into ADE (or Load Stock Data - see below) then ADE will generate a micro exclusion rectangle for each object such as a library object or generic building. This has the effect of excluding the stock object from the stock airport so that will not display. At the same time ADE creates its own copy of that object which is what you see in the ADE display and the one that appears in the sim. So the actions carried out for you are
- Exclude the stock object so it will not be shown in sim
- Replace it with a copy which is what shows in the sim
Now if you delete the object you can see in ADE (the copy) then it will no longer appear in the sim and neither will the original in the stock file. This is a much safer and cleaner method than placing a large exclusion rectangle over an area of the airport since that can cover objects that you don't want removed. Adding your own exclusion rectangle would remove the ADE copy and not the original which is already excluded.
The second point is that exclusion rectangles that overlap one another are known to cancel out so that the object actually re-appears.
ADE creates very small exclusion rectangles which only cover the reference point (placement coordinates) of an object. This tries to make sure that no unintended objects are also excludes.
Some users who load an ADE created bgl file will then see the micro excludes as small yellow rectangles. Not knowing what they are users have sometimes deleted them. This of course will allow the stock object to be displayed.
So unless you have a very good reason for using your own exclusion rectangle you should not. You should also never work from the bgl file but from the project file.
Those reasons could be that the airport was created by a third party and it contains object placements from the developer. Generally if an object won't get excluded then you need to understand why. It might be coming from a bgl file that loads after yours and so your exclusion rectangles will always be useless since they load after the exclude which is designed to remove them. Exclusion rectangles only work on objects in bgl files that FS loaded before it loaded the bgl file containing the exclusion(s). FS has a strict loading priority:
https://scruffyduck.screenstepslive.com/s/help_docs/m/20268/l/199760-priority-matters
Now if you are working on a third party or other bgl file that contains stock objects which are not being excluded then you can use the option to Load Stock Data into the project:
You can then select which type of items you want to load:
This should bring objects back in that are missing and also create excludes. So now you can delete the objects you don't want and let the ADE micro excludes do their job.
Sometimes it can be helpful to start clean with stock objects in which case you can use the Remove Stock Data function followed by the Load Stock Data function.
It is always wise to make a copy of the project file before carrying out this work in case it doesn't works as expected.
So back to my original question - why do you need to use your own exclusion rectangles?