After Effects Changing Files Mid Way of Animation

From the screenshots you posted below:
The icons on your layers look like image sequences - which is why they say filename[1-2].ai. 

Because of the way you imported these, After Effects thinks it's a piece of footage, and not an actual Illustrator file. 

Select the asset in your Project panel, right-click: Replace Footage > File

Navigate to the original file and make sure when you select your .ai file, that you UNCHECK any indicator marked "image sequence."

Because your files end with a number, AE assumed it was an image sequence. Sometimes helpful, but sometimes very confusing if you don't know that's what happened!

Well, none of your other layers appear to have any proper animation or trimming, so I'm pretty sure you're simply seeing your other layers popping in. Anyway, your screenshots still don't tell us much. You need to reveal the other layers' properties as well and then perhaps someoen can make sense of what's going on.

Mylenium

Please provide a sceenshot of your Ae timeline.

Without any specific info about your AI artwork, screenshots of your timelien and so on we can't tell you much. Looks perfectly normal if one were to assume that there are complex interactions of the paths in the artwork. and that very likely is the answer - you may have to re-oraganize the structure of the AI file and/or the layers and shapes created from it in AE to reproduce the intended look.

Mylenium