You have not properly prepared your Illustrator file. You ended up with a group, a bunch of paths, and probably some compound paths. Only simple paths without gradient fills can be converted to shape layers. You must dig into the AI file and determine which paths are convoluted. You might be better off selecting the Group created by Image Trace, then using the Layer Panel menu to Release to Layers - Sequence. Then you can dive into the AI file and figure out which paths may be giving you problems.
Unless you plan to use the C4D rendering engine and extrude the logo, you need to use Shape Layer Animators to modify the paths or animate the vector paths; there is no advantage to converting the Vector layer (AI file) to a shape layer.
You might be better off releasing to layers, grouping shapes by color in separate layers, and opening the converted file as a composition retaining layer size. Then you could animate each element in the logo individually, would not have to convert every path to a shape layer, or even any of them, and have the ability to do just about anything you wanted with the pieces.
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