Given that things like this can take quite some time to fix I wanted to provide a simple workaround for anyone else that happens to run into the issue and across this report.
The caveat is that this method highlights three more bugs that I've run into but they're minor compared to a high chance of a crash.

Workaround:

1. Create a new Object Layer and a new Shape Layer for each Fill.
2. For each Shape, make a copy of it on each Shape Layer at the same position so that the Shapes are overlaid.
3. Select which Object Layer you wish to Fill, Select the Shape on the corresponding Shape Layer, and Fill with desired Objects.
4. Save once both fills are done to not lose any progress.

Example of Layers
Objects:
Foliage_Tree_Objects
Foliage_Bush_Objects

Shapes:
Foliage_Tree_Shapes
polygon_1:

Position X=200000.000 Y=0.000

Foliage_Bush_Shapes
polygon_1Copy:

Position X=200000.000 Y=0.000

Bug 1: When two identical (nearly identical?) Shapes are overlaid on the same position one of them is difficult or sometimes impossible to Left-Click select.

Solution: Drag select to highlight one of the Shapes vertices which allows you to select the shape as a whole.

Bug 2: Small Shapes are even more difficult to select and in some cases drag selecting vertices will not work.
Solution: Drag select ALL Shapes in the area of the Shape you wish to select. Then deselect the Shapes you don't want with Shift-Left Click leaving just the Shape you want.

Bug 3: Some Shapes will cause a crash when filled no matter what. I'm unsure if this is related to the terrain the Shape is generating on or the Shape itself.

Solution: Delete the existing Shape and make a new Shape to be something similar and hope for the best.

Unrelated to all of this I noticed occasionally the Fill tool will use the same seed to generate objects thus placing objects in the exact same spots. Undoing the Fill or opening and closing the project and trying again fixes it.
While not explicitly a bug a seed option would be ideal.