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What is likely occurring is that the cut is being applied to another part in the assembly, for which the cut was not intended.
This is usually caused by using the "automatic" option to select the components that are to be cut.
However, Pro/E's auto-select algorithm will often include parts that are near the cut, but are clear of the cut.
The warning is just that, a warning. The cut will work fine.
However, Pro/E wastes regeneration time and memory (creating a pseudo-instance) attempting to cut such parts.
Therefore, I recommend that the "automatic" option never be used.
Gerry Champoux
Williams International