It looks like a transfer mode (blend mode) issue. In Illustrator the gradients are blended in "screen" mode whereas in After Effects the blend mode is "normal". If they are separate layers, you should be able to change the transfer mode. If not, you'll have to separate them first.
This thread is pretty old but it addresses an issue i'm trying to sort out: I am able to import AI artwork into AE and gradients appear correctly, but what I want is to take the path data from Illustrator AND apply the same gradient style in AE. Is this even possible?
I have tried copying a path from Illustrator into a shape layer, the path comes across but there is no fill (or gradient) data copied. Alternatively, when I import the AI file and select "Create>Create Shapes from Vector Layer" the corresponding new shape layer is created with the correct path, but the fill is a solid grey.
I did not create the original artwork. I would like to animate the art using path morphing, but there is a LOT of gradient information in the AI file and re-creating in AE will be very time consuming.