My guess is that you've done something to the clips in Premiere Pro that is causing this change in behavior. An unaltered clip in Premiere Pro will come across as a clip/layer in After Effects, but---for example---a clip that uses certain effects or the Scale To Frame Size option will come across as a precomposition to encapsulate those changes.
So I used Scale to Frame Size.
Thus the precomping.... Er..... Why would this put it into a precomp?
How about calling it 'fit to comp', like AE, and have them do the same thing, without the precomp feature?
The idea of having software tools in a product line is that they kinda work the same way. Like a common metaphor...
So why don't they work the same?
I'm going back to using these tools after a while away from front-line VFX.
There's a lot of stuff that between these two apps that seems really kinky.
Like there's now a great colour corrector in PR, but you can only add it in PR, even though it would be kinda super-handy in AFX.
But you can kinda add it when you convert the project, but you kinda don't get the interface.
And then all the effects are grouped differently. Like PR is a few versions behind... and ahead at the same time....
This doesn't feel like complicated stuff, surely?
If it's legacy support, isn't it time to standardise under the shiny new CC banner?