Why WAF disassociate resource when Cloudformation change resource Cloudfront?

What changes are you making to your CloudFront Distribution resource in your template? Are you attaching WAF separately to CloudFormation? If you modify a property affecting WAF, CloudFormation may overwrite it; if you modify a property which requires replacement, CloudFormation will replace your Distribution with a new one.

I'd recommend you use CloudFormation to associate AWS WAF with your Distribution. You can provide it using the WebACLId property of the DistributionConfig property in your template. If you don't want to manage the whole WAF through CloudFormation, I'd recommend making a Parameter in your template to allow you to specify the WAF ACL Id, and then use that parameter when setting the value in the Distribution resource.