Duplicate the layer a couple of times, mask it with feathere masks, mov it in place on top of the bad regions. Add some adjustments to blend colors.
Mylenium's suggestion is a good, simple one for some circumstances. If it doesn't work for your case, post a sample video (or at least screenshots) so that we cn give you more focused advice.
> I have very limited knowledge of AE and have just been asked to do this job.
Start here to learn After Effects.