Sorry, I'm unclear on the problem, and the image you've posted is fairly low res.
At a guess, you've imported a multi-layer Illustrator file, and you're getting opacity problems on some of the layers.
Do all the layers have 100% opacity in Illustrator before you import to AE?
Please click on the image to get the full view.
Yes i have imported a multi-layer illustrator file and all the layers have 100% opacity before importing to AE.
If purging all memory and cache does not solve the problem then select the layers that are giving you problems and at least one layer that is not giving you problems then press the "u" key twice to reveal all modified properties. If that does not give you a clue what's going on try soloing one of the layers with problems. If that does not help then select the layer and press Ctrl/Cmnd + e to edit the original and look at the layer in Illustrator. Carefully check the appearance and all other properties in AI to make sure there is nothing wrong there.
Start by turning off the motion blur. You may have some animation and the accumulated samples cause this effect. Then debug your project as Rick said. And of course also check your artwork in AI. You may have used blending modes and opacity trickery there that interferes.