Check with your carbon bike maker. Some recommend against using them in trainers as the side forces may cause cracking. BMC is one such company. http://www.bmc-switzerland.com/au-en/support/carbon-care/

And Felt has this to say on the matter: Felt cannot officially recommend using any trainer that the frame mounts to, all-out efforts can cause side load on the thin seat stays that they were not designed to handle. If the frame breaks this would not be a warranty.

Felt knows that many riders will use a trainer either in a warm up situation or in a bad weather/dark outside situation. We know Felt pros even do this. It has to be done correctly and the rider needs to know the bike was not designed for it so you have to be easy (no standing sprints for example). Some trainers are better than others but we do not know how hard it will be ridden, how often or the weight of the rider. The ones with side to side movement are much better vs. the rigid locked ones. The Felt engineers want to design bikes for the best possible riding feel on the road and do not want to compromise the ride to by making them optimal for every trainer.

Although, one the other hand , there are many people who use carbon bikes on trainers for years without any issues.