I use AI to create assets to animate in AE. As a matter of good practice I save my AI files in iterations, often with the naming convention:
I keep all my AI files in a folder (windows machine) until I'm happy with the illustration to be animated. I then set up my AE project and import the final AI file as a composition (retained layer sizes). The frustrating thing is that when I select, say example_V3 to import, AE always reads example_V1 in the folder. Without fail AE can't recognise that V1 and V3 are different files and always defaults to opening the first file in my hierarchy, even though they're clearly named differently (be it only the numerical digit). Why is this? To solve this I usually name my final file example_FINAL and then it pulls in the completed illustration and not one of the work in progress files. This seems like an elementary fault of reading files names. Give it a go and see if you get the same result...
Has anyone else ever noticed this and are Adobe aware of the issue? It's no biggie really but it's a bit annoying.
You have possibly simply enabled the sequence option in the file dialog. if that's not the case, you will have to provide at least soem system and version info, which you haven't done so far. if it's a bug, it's version specific, not per se a generic issue.