Well, a bit like is it fair that you are claiming money from him when he shares custody and costs 50:50? I don’t think it is, from what you have said.
Moreover, I think you are only able to claim cms, despite the 50:50 custody split (where normally you can’t) because you get both children’s CB and can use this as evidence that you are the primary carer for both children. Without that you would not be able to claim anything from your exHusband in terms of CMS. Arguably, this is not actually accurate and as you are able to claim CMS on the basis of this inaccuracy quite possibly unfair towards your partner (as per the rules).
As a result, your ex-husband is now only seeking what he is entitled to- a split of CB- in order to make sure you can only claim what you are entitled to, in turn.
Your ex-husband may have been happy to let you claim both before, as you (and your children) got a benefit from doing so, whilst he would not. However, once you used that to your advantage against him, he has clearly decided that he has to correct the inaccuracy in order to ensure an accurate assessment can be made as to each of your entitlements from the state and each other. Which seems pretty “fair” to me.
In short, you decided to “game the system” by using your CB claim for both children, which he had not sought to gain despite being eligible, in order to claim (inaccurately) that you are the primary carer despite a 50:50 custody and costs split. Thus, you appeared to be eligible to claim CMS from him, due to your status as a primary care for both children, when in fact, the rules would state that in a custody arrangement such as yours, you are likely only going to be eligible to claim for one child. It is likely you will lose CB payment and cms for one child, but may indeed get cms for the other (plus their CB payment). I imagine any amount of cms you have to pay him would be minimal given your income.
You pushed for everything you thought you were entitled to. It now looks like that is exactly what you will get. I think you may get more in CMS than cB anyway, so may not be a net financial loss.