I can see in the resultant CSR that is created and used these requested properties are seemingly set correctly as the CSR includes: Signature Algorithm: ecdsa-with-SHA256
However the resultant certificate that's issued has Signature Algorithm: ecdsa-with-SHA384
Your key is P-256. Let's Encrypt has signed it with a P-384 intermediate. You control what key you're using, and Let's Encrypt controls what key they're using.
Other than it being a little confusing, is it causing any actual problems for you?