Do you mean the stem of the fruit, or the stem of the plant?
I had the stem go underneath one of my crosses a few years ago, before it had grown the fruit. I cut off the stem above the rot and put it on a windowsill in a pickle jar of plain water. No nutes provided but the darn thing actually grew the fruit and produced six seeds!
I grew that cross out this year and five of six seedlings were vigorous brutes now loaded with fruit and F2 seeds.
I have noticed that crosses on side shoots later in the season are sometimes hard to get growing. The plant just doesn't want to put its energy into the side fruit. Worst of all are suckers from low on the plant. So choose a main stem or a strong side stem from higher up the plant to bear your cross, for better chance of success.
Also some plants are reluctant cross mothers, and will reject and refuse to grow the ''tampered' blossoms. Reciprocal cross can be a workaround if you're not sure which parent would be the better mother. It is even worth it to make random crosses just to see which of your parent candidates make great mothers or not - and of course, it's practice.
If your cross is one of the later fruit in a cluster, it may be rejected as well.
So, for best chance of success, I will choose the first two ready blossoms to emasculate in an unopened cluster. I mark the whole cluster instead of adding stress by hanging something on the cross itself. And do the cross two times - one or other may take.
I do let them set the extra fruit if they want to, but some people will remove everything else that could compete for nutrients in the cluster.
Good luck!
