Issues with elastic index templates

We are using index templates to define mapping, and we create more than 200 indices every day and we have defined templates for all of them.
And depending on need we keep updating templates to add additional alias/fields/filtering, and in few instances we have seen a behaviour of these getting to the previous definition of the template. Any help on how I can debug will be great.

P.S: The exact template if reapplied will work again, but randomly we see this behaviour. And this is not a limited any particular index template