the withdrawal of excess contributions is supposed to include earnings thereon. they have to be withdrawn by the due date including extensions. any amount not withdrawn is subject to a 6% penalty. the problem is that you have taken a distribution and we don't know exactly how that was handled. if you requested a normal distribution of $X, then the trustee might report it as such and if it didn't cover qualified medical expenses, it is subject to penalties. your going to have to discuss the situation with the custodian/trustee so to minimize any penalties.
