When using a negative buffer value on too small polygons, they are always output as rejected features (since there is no valid part of the polygon to output).
Is there a way to filter beforehand such that these features aren't rejected?
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If your aim is to keep the original geometry where the buffer cannot be applied, you could extract the geometry to an attribute prior to the bufferer then rebuild the geometries from that attribute for features exiting the rejected port.
This may not be what you're after but in case you didn't know, you can change the way rejected features are handled so that the workspace doesn't fail. To do this you can change a Workspace Parameter (in the Navigator pane on the left) to continue the translation when features are rejected.
Use the area calculator to extract the area into an attribute then filter on the size (if you know the min size of the features you want to buffer) using the tester. The fails will be the small ones with original geometry.