More than likely not. Your body is probably reacting to the implanon.
when i got implanon in, i was taking birth control pills for a further week and told to make sure to take precautions within these seven days as to avoid this situation. the pregnancy test you took before you got the implanon would be unrelated to having sex AFTER getting the implant inserted. the morning after pill is more effective the sooner you take it and you should have taken it saturday, sunday & monday, the days after you had sex. your body would not instantly adapt to having the implant in so these may be pregnancy/fertilisation symptoms. You should go back and speak to your doctor as to what to do. you obviously do not want to be pregnant which is why you are taking precautions so just be more careful if you are not pregnant this time
When I got the paraguard iud they told me it was its own form of the morning after pill and that you should be able to have sex unprotected right after getting it. Not sure about other types though.