I think I might have found out why.
I've included my previous spouse visa home office reference number in the do you have any home office reference numbers?
Ah, okay. You will not have any Home Office reference numbers, because those are only issued if you have an in-country visa refusal or you make an appeal, or you are an asylum seeker/refugee etc.
So, that number should have been left blank, though using your previous application number probably won't be an issue.
The heath surcharge reference number is from my previous application.
Will that be a problem?
Yes, that will be a problem. The previous reference number was only valid for your previous application... because it only covered your healthcare for the length of the spousal visa and not for your FLR(M) visa.
So, for this visa, you need to pay again and get a new IHS reference number, to cover your healthcare for the next 2.5 years.
As I said though, it should be a simple fix. They can't process your visa until you provide them with the new IHS number, so just go and pay the IHS surcharge, get the new number and include it somewhere in your application. As long as they have the new reference number, all will be fine.