Using Overlord to import an AI shape with a clipping mask into AE

Duplicate the Objects that are part of the Illustrator Clipping Mask for reference and then lock them and hide their visibility.

With the originals, release the Clipping Mask and bring them into After Effects as separate Layers and then set a Track Matte.

It sounds like the Illustrator file was not properly prepared to be used in After Effects. We need workflow details and a screenshot of the AE and AI workspace showing the problem layers to suggest a viable solution.