HI, I had exactly the same experience - filed my spouses', and then mine was rejected. I have previously explained what I did to make it go. But it may be, if you do what I did, that your spouse's tax due may change somewhat.
We should not have to do this - it goes back to the Govt reversal of how to treat Cap Gains, plus TTx dropping the ball, but it works and the CRA should be OK with it.
First, enter 1/2 of each T3 into each of your T1s separately, showing 100% ownership of 1/2 of all values (or whatever % split is appropriate). Second, I entered no values in box 52 and the same number in box 53 as in box 21. BMO Investorline suggested doing this, actually.
TTX should then calculate correctly with respect to your T3s for both returns.
In your case, you might then see whether your spouse's taxes change. If so, you should alter key values via the CRA site after you get a provisional notice of assessment message back from them.
Good luck.
