I have seen this happen many times and it has happened to my 987 Boxster as well, when you put the top down and put the top back up some may experience the sides of the top not going back to its proper position which is behind the metal side frame, as you can see on the picture below the outer edge of the top does not go back in its original position.
First issue is if you put the top halfway down you will notice a grey string that is attached to the metal frame with a screw, that string looks like a shoe lace, see the picture below.
Please note that on the picture below the top is not halfway down but it clearly gives you an idea of what to look for.
Now this cable takes care of the upper side of the top, if or when you fix it your top experiences the same issue it is because the lower portion of it needs to be repaired as well. So let's move one to the 2nd problem.
Sorry no pictures available for this problem ,but I'm sure you will find your way with the following description. The 2nd problem is caused by an elastic band that is attached with a screw to the metal frame of the top, if you put your top a little more than halfway down you will notice an elastic strap that runs from the edge of the top to inside the top close to the far right or left of the window (depending on which side you are working on) you will notice that the band has stretched and it no longer pulls the channel back in , at this point you will need to remove the screw that holds the elastic strap , you will need to use a short torx screwdriver in order to get to it, space is limited as you are working inside the top between the headliner and the actual top so patience is needed , once you remove that screw you will notice that Porsche as made several slots on that strap, looks like they were being pro-active and were anticipating the problem for the future, to get this elastic band you will need to move 2 notches up and re-attach the elastic band with the screw. This will fix your problem.