Hello dear
Understand your concern.
Implanon is type of long-acting reversible 
contraception, the most effective form of birth control.
It inhibits the ovulation and 
implantation..
Common side effects of implanon are below:
Irregular bleeding and spotting: Delayed period, dysmenorrhoea
weight gain 
Ovarian cysts
Acne
So I think it may be side effects.
It is generally due to hormonal imbalance
If not resolved
You can consult the gynecologist:
Do the full hormonal profile like E2, FSH, LH, pogesterone, HCG, 
Prolactin, Thyroid profile.
If necessary 
endometrial biopsy, follicle study and USG.
If bleeding is excessive consult the Gp and you can remove it and then consult the gynecologist 
Hope this may help you.
Best regards
Dr. Sagar