You are not alone. There have been several suggestions put forward on this blog.
The one that I followed was: Delete the T3 capital gain from Box 21 & 53, checked that there was nothing on Schedule 3 line 17600 or T936 line 68140, saved the return and went through the Net File process. Success.
I had a capital loss on T5008 so no effect on the refund - but it will affect the capital loss carryforward. I will wait until CRA issues their Notice of Assessment which may adjust for the missed capital gain or will file an adjustment then
