Strange bug in imported .ai file

I've imported an .ai file with two layers, animated with puppet pins – looked fine.

Later I notice there's something weird going on with the layers. It looks as it should in Illustrator.

I tried masking out those "extra bits" but even the mask acts odd and cuts off part of layer inside of it.

I saved a new version of the .ai file and replaced both layers in the comp which sort of worked on one. The other comes out even more strange looking!