I have been having troublefinding someone to remove my implanon and so it has now been in for 3 years and 9 months. Is it possible that doing this has caused any harm?

No, but go to your GP they will probably remove it, if they won't then a family planning clinic will.

Sometimes they say if it stays in too long etc it can cause eptopic pregnancies and also infertility. So its best to find somewhere :)