Uncomfortable during sex. In future?

Hi During annual medical check up in sep'17, gynaecologists told that there is slight infection in Vagina and she gave some medicine which includes tablet as well as to insert for 5days, after that just few days back my wife had pre medical check up in that also the same problem informed by doctor and given medicine as tablet only. My wife discussed this with me and told me that every time during sex she feel uncomfortable but this only happen when I am on upper side and if she is on top then she doesn't feel. We got married just before 11 months. She has normal periods but bleeding stops normally on 3rd days and little on 4th day, she has cycle of 26-27days. Please let me know how should I proceed. Is it because of age or some harmon changes or is there any problem with pregnancy also in future?