The excess contribution is present in whichever account you designate as the one containing the excess. By requesting a return of excess contribution from your HSA, you've designated that the excess contribution was made to your HSA, not your in wife's HSA, so the gain must be determined by the investment performance only in your HSA.
In this case, the gain is determined by the investment performance in your HSA between the time of your 3/31/19 contribution and the date of the return-of-excess-contribution distribution (also taking into account in the calculation any intervening regular distributions). Investment performance in your wife's HSA is irrelevant to a return of excess contribution from your HSA.
How is it that the HSA custodian did not properly calculate the attributable gain and include it in the distribution? It's generally their responsibility to do so. Without that being included in the distribution, the distribution does not meet the legal requirement for the distribution to be a return of excess contribution. A code 2 Form 1099-SA for a return of excess contribution must show in box 2 the proper amount of gains.
If your employer does not exclude from box 1 the amount of the the returned excess, you don't include the returned excess in income again, you only include the attributable gains.
