You should have requested an explicit return of excess contribution and your HSA custodian should have been obligated to calculate and distribute the gain-adjusted amount. The gain is subject to income tax but not to any penalty. The excess itself is also subject to tax if it was contributed through your employer such that your employer will exclude it from box 1 of your W-2; if it was a personal contribution it simply won't be deductible.
It sounds like you are saying that the attributable gains have not been distributed. Why didn't that happen? Did you mistakenly request a regular distribution instead of an explicit return of excess contribution? That would be problematic. If so, has it been less than 60 days since you obtained the regular distribution?
Given that your HSA had gained about 10%, resulting in the adjusted amount required to be distributed to be about 110% of the excess contribution and the gains in your wife's HSA were less, it might have been better to treat the contribution made to your wife's HSA as the one that was excess and request that that one be returned instead.
