Although some people may be allergic to the latex, plastic or spermicides used in condoms, there are no medical side-effects from their use. Those who have an allergy will find that they are readily available in other materials or without spermicides.
Condoms are very flexible, but they can tear, split or come off if not put on properly. So you should learn to do this. Some people say that they interrupt the flow of sex or lessen sensation, but this may be down to the type of condom used or when you put it on. Try out different brands and make putting on a part of the sexual activity if you can.