Hello.
As the title said, object with opacity less than 100% became less than that when masked. In the example provided:
Two sets of examples, the top row and bottom row.
The top-left circle has black fill and opacity of 50%, the middle circle has the same fill and opacity, but masked. The result is a lighter color, same as the right circle with black fill and opacity of 25%.
The bottom-left circle has black fill and opacity of 25%, the middle circle has the same fill and opacity, but masked. The result is a lighter color, same as the right circle with black fill and opacity of 6%.
Most likely the opacity became squared after masking: For the top example, 0.5 * 0.5 = 0.25 -> 25% and for the bottom example 0.25 * 0.25 = 0.0625 -> 6.25%