Hello, I have also had this problem... I noticed the roof going a bit thin on either side and thought the same as you that it was catching the rubber seal.
I was told by the guy at my local dealer that there was nothing to worry about and that it would probably not get any worse therefore sent me on my way.
I was not that pleased with that and it was bothering me so I took it to another dealership, by this time the warranty had expired.
It was confirmed that there had been a problem from manufacture with the roof vibrating against something while the roof was in the storage position ie roof down.
Now because the warranty had run out they offered to replace the roof with goodwill however I had to pay half the labour cost, £450.00.
Although I complained to customer services I still had to pay...
I bought my Z4 as a pre-regerstered / demonstrater with about 2000 miles on the clock and because I do not clock up many miles it took a long time for this problem to appear. It is a 07 car and it only has 14k on the clock now.
Regards Jeff... I also had a problem with water getting in through the passenger side door seal...