Bounty showing up even though kills were hidden

Crime Witness

Bounty witness is not the same as combat detection, combat detection is affect by sneak skill, invisibility, light etc but witness is by LOS. Therefore there is a chance that your kill is witnessed by another person but he/she is unable to see you in combat.

This can be prevented by cutting the LOS by covering nearby NPCs with baskets for similar item before committing the crime, or waiting for the target to be clearly isolated before killing.

Clearing Bounty

Bounty of killing can be removed by silencing all witnesses, if you remember where you got the bounty from you can return and kill possible witnesses near the area and if you managed to kill all who witnessed your crime the bounty will clear - careful not to accumulate more in the process.

If the witness is essential and cannot be killed you can go to jail and serve your term by talking to any guards of the hold, since your level is low the amount of exp in each skill to be lost during jail term will probably not be too much. Alternatively you can pay your own bounty with any guard but remember to stash any stolen item before you do or they will be confiscated.