The clone stamp tool has several options. You must look through each frame and make sure you have fixed the problem. It the repair is not showing in the AE comp then you didn't use the tool correctly. I'd search for some tutorials. There are several good ones out there.
If it's still showing in your comp, what makes you think you removed it with the clone stamp tool?
If you're only using AE for this one thing, why not just copy and paste the video clip from Premiere into AE, do your clone work, then render it out in an intermediate codec, and use it in Premiere?
Agree with the others. your post is far too vague and it's very likely that you used the tool with the "current" frame option which does exactly what it says - clone only on the current frame. Anyway, this is like blind people talking about different shades of blue, so by all means do provide screenshots and an exact description of what you do as well as system info.
I wasn't using the current frame option, it was set to constant, however just to explain:-
I was using Prem pro and replaced a clip via the dynamic link to AfterEffects, the layer it automatically put in the composition was the actual .mov clip. This clip had an object I wanted to remove, which I did using the clone tool, however this did not replicate in the composition. I ended up creating a new composition and imported the same clip, carried out the same procedure and it worked OK?