I think you will have to  contact support for an answer.

Had your opponent sent troops to attack your SH while you had troops there the opponents would have scored points in the Killing enemy warriors during an attack category.

Perhaps what happened is that you initiated a siege at your Tower of Odin and then put troops into the SH as reinforcements and awaited events.  Your stronhold was then attacked but not by your CvC opponent.  You recieved one or more reports to show that your troops had engaged in battles and had been killed while also killing some of the scouts and warriors which attacked.  By the time the first (and subsequent) Jotunn march reached your SH no troops remained and no battle was fought.  You score CvC points by fighting battles with Jotunn troops and your CvC opponents' troops but you do not score CvC points for SH battles with others.

To give your clan a better chance to avoid this you and your clanmates could put reinforcements into the SH only shortly before a Jotunn march is due to arrive.  With luck your troops will then engage the Jotunn troops and points will be scored.  You recall the surviving troops and put troops back into the SH just before the next march arrives.

Good luck.

Thanks for explaining that John, I did still have troops when the Jotun warriors arrived but that is a really good point to wait to send troops till they are a minute away. My alliance clan got the points but I did not. I still won the CVC though so I guess it doesn't really matter at this point.

I have seen no analysis as to how kills, and therefore CvC points/soul shards, are calculated by the game.

Assuming SH battles are calculated in the same way as other battles the game first calculates which army is the "larger".  That is partly a matter of numbers but also a matter of unit strength.  The larger army wins and inflicts 80% casualties on the loser.  A second, complex, calculation then determines the casualties suffered by the winner.

In an unsuccesful SH defence 80% of all the defending troops will be lost and the kills achieved will presumably be distributed evenly with higher numbers of kills attributed to stronger troops - and troop type playing a small part depending on the make up of the attacking Jotunn troop.

In a succesful defence I take it that the calculation of casualties sustained also determines which troops made kills.

Exactly how that calculation could result in all the kills being attributed to your ally's troops and none to your troops I do not know but I suspect that your ally may have put a lot of low tier/low strength troops into the SH while your surviving troops were all of a higher tier/strength.

In case that is correct you might try agreeing with your ally what tier/strength of troops you will each contribute and perhaps that will bring about a more equitable distribution of points and soul shards.