Struggling trying to use 'Create Shapes from Vector Layer' in After Effects to animate my Logo

OK so my first question is why do you want to use the convert command in After Effects in the first place. It isn't necessary to convert imported vector files to shapes unless you specifically need to use one of the features that only work with live shapes. Things like Repeater, or the animated stroke functions that can only be applied to AE shape layers are two examples that come to mind.

Activate the Direct Selection Tool (the white arrow) and click on one of the shapes.

When you see the anchor points in Illustrator are they only around the rectangular bounding box the graphics have or are they on the contour of each of the shapes? If they are not on the contours of each shape then the shapes are probably not vectors.

If they are vectors one of the problems with the conversion command in AE is that there are many types of graphics that Illustrator can make that are not supported for conversion (gradients, and complex clipping masks for example, complex compund paths) or other that dont convert well (like patterns). So it could be that.

Also keep in mind that live text in illustrator isnt' covered by that conversion command in AE only vector shapes. If you have live Illustrator text you would have to turn it into outlines (the command is in the text menu).

If you want to link it I can take a look at your Illustrator file and give you more detail.