macOS Sierra 10.12.6
MacBook Pro 13" 12,1 (early 2015)
2560 x 1600 Retina
Intel Iris 6100
Pixelmator 3.6 Cordillera (61103)
1. Create a new image 75 x 75 pixels
2. Resize canvas to 100 x 100 pixels
3. Show Grid
4. Select the shape tool and choose the cog shape. It has a fill color by default.
5. Draw out the cog shape and make sure its edges are flush with the white background. No white pixels should be showing between the edges of the shape and the transparent canvas. The shape should be 75 x 75 pixels.
6. Now trim the canvas using Image -> Trim Canvas... and use default options (transparent pixels)
7. When the canvas is trimmed down to 75x75 the fill color of the cog shape turns off. Only stroke is visible.
8. Selecting gradient fill on the shape works as expected
9. Select color fill again
10. Grab one of the corners of the shape and reduce the size
11. Eventually the fill color is enabled again
I have tested this with the "house" and the "pentagon" shape as well so I guess it affects all or most shapes.
I was able to reduce the size of the shape to activate the fill color again and then increase the size again to 75 x 75 pixels and the fill color will sometimes stay activated so I could work around the problem. I just tried a few times using different corner drag boxes.